Galaxy |

Changeset 0:f493979f1408 (2016-12-21)

Commit message:
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty

diff -r 000000000000 -r f493979f1408 Bam.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Bam.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,81 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Class to handle Bam files to UCSC TrackHub
+"""
+
+import logging
+import os
+import shutil
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class Bam( Datatype ):
+    def __init__(self, input_bam_false_path, data_bam):
+        super(Bam, self).__init__()
+
+        self.track = None
+
+        self.input_bam_false_path = input_bam_false_path
+
+        self.data_bam = data_bam
+        # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
+        if ".bam" not in self.data_bam["name"]:
+            self.name_bam = self.data_bam["name"] + ".bam"
+        else:
+            self.name_bam = self.data_bam["name"]
+
+        self.priority = self.data_bam["order_index"]
+        self.index_bam = self.data_bam["index"]
+        # TODO: Think about how to avoid repetition of the color treatment
+        self.track_color = self.data_bam["track_color"]
+
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = self.data_bam["group_name"]
+
+        # First: Add the bam file
+        # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
+
+        bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
+        shutil.copyfile(self.input_bam_false_path, bam_file_path)
+
+        # Create and add the bam index file to the same folder
+        name_index_bam = self.name_bam + ".bai"
+        bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
+        shutil.copyfile(self.index_bam, bam_index_file_path)
+
+        # Create the Track Object
+        self.createTrack(file_path=self.name_bam,
+                         track_name=self.name_bam,
+                         long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
+                         track_file=bam_index_file_path,
+                         track_color=self.track_color,
+                         group_name=self.group_name
+                         )
+        #
+        # dataURL = "tracks/%s" % self.name_bam
+        #
+        # trackDb = TrackDb(
+        #     trackName=self.name_bam,
+        #     longLabel=self.name_bam,
+        #     shortLabel=self.getShortName( self.name_bam ),
+        #     trackDataURL=dataURL,
+        #     trackType='bam',
+        #     visibility='pack',
+        #     priority=self.priority,
+        # )
+        #
+        # # Return the Bam Track Object
+        # self.track = Track(
+        #     trackFile=bam_index_file_path,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bam %s created" % self.name_bam)
+        #print("- %s created in %s" % (self.name_bam, bam_file_path))
+        #print("- %s created in %s" % (self.index_bam, bam_index_file_path))

diff -r 000000000000 -r f493979f1408 Bam.pyc

Binary file Bam.pyc has changed

diff -r 000000000000 -r f493979f1408 Bed.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Bed.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,73 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+# Internal dependencies
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class Bed( Datatype ):
+    def __init__( self, inputBedGeneric, data_bed_generic):
+        super(Bed, self).__init__()
+
+        self.track = None
+
+        self.inputBedGeneric = inputBedGeneric
+
+        self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+
+        self.data_bed_generic = data_bed_generic
+        self.name_bed_generic = self.data_bed_generic["name"]
+        self.priority = self.data_bed_generic["order_index"]
+        self.track_color = self.data_bed_generic["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = self.data_bed_generic["group_name"]
+
+
+        # Sort processing
+        subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
+        trackName = "".join( ( self.name_bed_generic, ".bb") )
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+        with open(myBigBedFilePath, 'w') as self.bigBedFile:
+            subtools.bedToBigBed(self.sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 self.bigBedFile.name)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_bed_generic,
+        #     shortLabel=self.getShortName(self.name_bed_generic),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed',
+        #     visibility='dense',
+        #     thickDrawItem='on',
+        #     priority=self.priority,
+        # )
+        #
+        # # Return the BigBed track
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bed %s created" % self.name_bed_generic)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))

diff -r 000000000000 -r f493979f1408 Bed.pyc

Binary file Bed.pyc has changed

diff -r 000000000000 -r f493979f1408 BedSimpleRepeats.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSimpleRepeats.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class BedSimpleRepeats( Datatype ):
+    def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):
+
+        super(BedSimpleRepeats, self).__init__()
+
+        self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
+        self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
+        self.priority = data_bed_simple_repeats["order_index"]
+        self.track_color = data_bed_simple_repeats["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bed_simple_repeats["group_name"]
+
+        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+
+        # Sort processing
+        subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + .bb
+        trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed4+12',
+                                 autoSql=auto_sql_option)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_bed_simple_repeats,
+        #     shortLabel=self.getShortName( self.name_bed_simple_repeats ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed 4 +',
+        #     visibility='dense',
+        #     priority=self.priority,
+        # )
+        #
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))

diff -r 000000000000 -r f493979f1408 BedSimpleRepeats.pyc

Binary file BedSimpleRepeats.pyc has changed

diff -r 000000000000 -r f493979f1408 BedSpliceJunctions.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BedSpliceJunctions.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class BedSpliceJunctions( Datatype ):
+    def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions):
+
+        super(BedSpliceJunctions, self).__init__()
+
+        self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path
+        self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
+        self.priority = data_bed_splice_junctions["order_index"]
+        self.track_color = data_bed_splice_junctions["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bed_splice_junctions["group_name"]
+
+        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+
+        # Sort processing
+        subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + .bb
+        trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) )
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as')
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed12+1',
+                                 autoSql=auto_sql_option)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # dataURL = "tracks/%s" % trackName
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_bed_simple_repeats,
+        #     shortLabel=self.getShortName( self.name_bed_simple_repeats ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigBed 4 +',
+        #     visibility='dense',
+        #     priority=self.priority,
+        # )
+        #
+        # self.track = Track(
+        #     trackFile=myBigBedFilePath,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bed splice junctions %s created" % self.name_bed_splice_junctions)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))

diff -r 000000000000 -r f493979f1408 BedSpliceJunctions.pyc

Binary file BedSpliceJunctions.pyc has changed

diff -r 000000000000 -r f493979f1408 BigWig.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/BigWig.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,62 @@
+#!/usr/bin/python
+
+import os
+import shutil
+
+# Internal dependencies
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+
+
+class BigWig( Datatype ):
+    def __init__(self, input_bigwig_path, data_bigwig):
+        super(BigWig, self).__init__()
+
+        self.track = None
+
+        self.input_bigwig_path = input_bigwig_path
+        self.name_bigwig = data_bigwig["name"]
+        self.priority = data_bigwig["order_index"]
+        self.track_color = data_bigwig["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bigwig["group_name"]
+
+        #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
+
+        trackName = "".join( ( self.name_bigwig, ".bigwig" ) )
+
+        myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName)
+        shutil.copy(self.input_bigwig_path, myBigWigFilePath)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bigwig,
+                         track_type='bigWig', visibility='full',
+                         priority=self.priority,
+                         track_file=myBigWigFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # dataURL = "tracks/%s" % trackName
+        #
+        # # Return the BigBed track
+        #
+        # trackDb = TrackDb(
+        #     trackName=trackName,
+        #     longLabel=self.name_bigwig,
+        #     shortLabel=self.getShortName( self.name_bigwig ),
+        #     trackDataURL=dataURL,
+        #     trackType='bigWig',
+        #     visibility='full',
+        #     priority=self.priority,
+        # )
+        #
+        # self.track = Track(
+        #     trackFile=myBigWigFilePath,
+        #     trackDb=trackDb,
+        # )
+
+        print("- BigWig %s created" % self.name_bigwig)
+        #print("- %s created in %s" % (trackName, myBigWigFilePath))

diff -r 000000000000 -r f493979f1408 BigWig.pyc

Binary file BigWig.pyc has changed

diff -r 000000000000 -r f493979f1408 Datatype.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Datatype.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,115 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Super Class of the managed datatype
+"""
+
+import os
+import tempfile
+
+from util import subtools
+from Track import Track
+from TrackDb import TrackDb
+
+
+class Datatype(object):
+
+    twoBitFile = None
+
+    input_fasta_file = None
+    extra_files_path = None
+    tool_directory = None
+
+    mySpecieFolderPath = None
+    myTrackFolderPath = None
+
+    twoBitFile = None
+    chromSizesFile = None
+
+    track = None
+
+    def __init__(self):
+
+        not_init_message = "The {0} is not initialized." \
+                           "Did you use pre_init static method first?"
+        if Datatype.input_fasta_file is None:
+            raise TypeError(not_init_message.format('reference genome'))
+        if Datatype.extra_files_path is None:
+            raise TypeError(not_init_message.format('track Hub path'))
+        if Datatype.tool_directory is None:
+            raise TypeError(not_init_message.format('tool directory'))
+
+    @staticmethod
+    def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
+                 extra_files_path, tool_directory, specie_folder, tracks_folder):
+        Datatype.extra_files_path = extra_files_path
+        Datatype.tool_directory = tool_directory
+
+        # TODO: All this should be in TrackHub and not in Datatype
+        Datatype.mySpecieFolderPath = specie_folder
+        Datatype.myTrackFolderPath = tracks_folder
+
+        Datatype.input_fasta_file = reference_genome
+
+        # 2bit file creation from input fasta
+        Datatype.twoBitFile = two_bit_path
+        Datatype.chromSizesFile = chrom_sizes_file
+
+    @staticmethod
+    def get_largest_scaffold_name(self):
+        # We can get the biggest scaffold here, with chromSizesFile
+        with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
+            # TODO: Check if exists
+            return chrom_sizes.readline().split()[0]
+
+    # TODO: Rename for PEP8
+    def getShortName( self, name_to_shortify ):
+        # Slice to get from Long label the short label
+        short_label_slice = slice(0, 15)
+
+        return name_to_shortify[short_label_slice]
+
+    # TODO: Better handle parameters, use heritance mecanism
+    # TODO: Use default parameters for some, like visibility
+    def createTrack(self,
+                    file_path=None,
+                    track_name=None, long_label=None, thick_draw_item='off',
+                    short_label=None, track_type=None, visibility=None, priority=None,
+                    track_file=None, track_color='#000000', group_name="Default"):
+
+        # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
+        data_url = "tracks/%s" % file_path
+
+        if not short_label:
+            short_label = self.getShortName(long_label)
+
+        # Replace '_' by ' ', to invert the sanitization mecanism
+        # TODO: Find a better way to manage the sanitization of file path
+        long_label = long_label.replace("_", " ")
+        short_label = short_label.replace("_", " ")
+
+        #TODO: Check if rgb or hexa
+        # Convert hexa to rgb array
+        hexa_without_sharp = track_color.lstrip('#')
+        rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
+        rgb_ucsc = ','.join(map(str, rgb_array))
+
+        track_db = TrackDb(
+                trackName=track_name,
+                longLabel=long_label,
+                shortLabel=short_label,
+                trackDataURL=data_url,
+                trackType=track_type,
+                visibility=visibility,
+                thickDrawItem=thick_draw_item,
+                priority=priority,
+                track_color=rgb_ucsc,
+                group_name=group_name
+        )
+
+        # Return the Bam Track Object
+        self.track = Track(
+                trackFile=track_file,
+                trackDb=track_db,
+        )

diff -r 000000000000 -r f493979f1408 Datatype.pyc

Binary file Datatype.pyc has changed

diff -r 000000000000 -r f493979f1408 Gff3.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Gff3.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,67 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+# Internal dependencies
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class Gff3( Datatype ):
+    def __init__(self, input_Gff3_false_path, data_gff3):
+        super( Gff3, self ).__init__()
+
+        self.track = None
+
+        self.input_Gff3_false_path = input_Gff3_false_path
+        self.name_gff3 = data_gff3["name"]
+        self.priority = data_gff3["order_index"]
+        self.track_color = data_gff3["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_gff3["group_name"]
+
+        # TODO: See if we need these temporary files as part of the generated files
+        unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
+        unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
+        sorted_biGenePred_file = tempfile.NamedTemporaryFile(suffix=".sorted.bigGenePred")
+
+        # gff3ToGenePred processing
+        subtools.gff3ToGenePred(self.input_Gff3_false_path, unsorted_genePred_file.name)
+
+        # genePredToBigGenePred
+        subtools.genePredToBigGenePred(unsorted_genePred_file.name, unsorted_bigGenePred_file.name)
+
+        # Sort processing
+        subtools.sort(unsorted_bigGenePred_file.name, sorted_biGenePred_file.name)
+
+        # TODO: Check if no errors
+
+        # bedToBigBed processing
+        trackName = "".join( (self.name_gff3, ".bb" ) )
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sorted_biGenePred_file.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+8',
+                                 tab=True)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_gff3,
+                         track_type='bigGenePred', visibility='dense',
+                         priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        print("- Gff3 %s created" % self.name_gff3)

diff -r 000000000000 -r f493979f1408 Gff3.pyc

Binary file Gff3.pyc has changed

diff -r 000000000000 -r f493979f1408 Gtf.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Gtf.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,156 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+
+# Internal dependencies
+from Datatype import Datatype
+from util import subtools
+
+class InfoModifiedGtf():
+    def __init__(self, is_modified=False, array_modified_lines=[]):
+        self.is_modified = is_modified
+        self.array_modified_lines = array_modified_lines
+
+    def get_str_modified_lines(self):
+        return ','.join(map(str, self.array_modified_lines))
+
+class Gtf( Datatype ):
+    def __init__( self, input_gtf_false_path, data_gtf):
+
+        super(Gtf, self).__init__()
+
+        self.track = None
+
+        self.input_gtf_false_path = input_gtf_false_path
+        self.name_gtf = data_gtf["name"]
+        self.priority = data_gtf["order_index"]
+        self.track_color = data_gtf["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_gtf["group_name"]
+
+        #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
+
+        # TODO: See if we need these temporary files as part of the generated files
+        genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
+        unsorted_bigGenePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsorted.bigGenePred")
+        sorted_bigGenePred_file = tempfile.NamedTemporaryFile(suffix=".sortedBed.bigGenePred")
+
+        # GtfToGenePred
+        ## Checking the integrity of the inputs
+        modified_gtf = self._checkAndFixGtf()
+
+        ## Processing the gtf
+        subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
+
+        # TODO: From there, refactor because common use with Gff3.py
+        # genePredToBigGenePred processing
+        subtools.genePredToBigGenePred(genePredFile.name, unsorted_bigGenePred_file.name)
+
+        # Sort processing
+        subtools.sort(unsorted_bigGenePred_file.name, sorted_bigGenePred_file.name)
+
+        # bedToBigBed processing
+        trackName = "".join( ( self.name_gtf, ".bb") )
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigGenePred.as')
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(sorted_bigGenePred_file.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+8',
+                                 tab=True)
+
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_gtf, track_type='bigGenePred',
+                         visibility='dense', priority=self.priority,
+                         track_file=myBigBedFilePath,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        # TODO: Use Logging instead of print
+        if modified_gtf.is_modified:
+            print("- Warning: Gtf %s created with a modified version of your Gtf because of start/end coordinates issues."
+                  % self.name_gtf)
+            print("Here are the lines removed: " + modified_gtf.get_str_modified_lines())
+        else:
+            print("- Gtf %s created" % self.name_gtf)
+
+    def _checkAndFixGtf(self):
+        """
+        Call _checkAndFixGtf, check the integrity of gtf file,
+        if coordinates exceed chromosome size, either removed the whole line(s) or truncated to the end of the scaffold
+        depending on the user choice
+        default: remove the whole line(s)
+        """
+        # Set the boolean telling if we had to modify the file
+        modified_gtf = InfoModifiedGtf()
+
+        # Create a temp gtf just in case we have issues
+        temp_gtf = tempfile.NamedTemporaryFile(bufsize=0, suffix=".gtf", delete=False)
+
+        # TODO: Get the user choice and use it
+        # TODO: Check if the start > 0 and the end <= chromosome size
+        # Get the chrom.sizes into a dictionary to have a faster access
+        # TODO: Think about doing this in Datatype.py, so everywhere we have access to this read-only dictionary
+        dict_chrom_sizes = {}
+        with open(self.chromSizesFile.name, 'r') as chromSizes:
+            lines = chromSizes.readlines()
+            for line in lines:
+                fields = line.split()
+                # fields[1] should be the name of the scaffold
+                # fields[2] should be the size of the scaffold
+                # TODO: Ensure this is true for all lines
+                dict_chrom_sizes[fields[0]] = fields[1]
+
+        # Parse the GTF and check each line using the chrom sizes dictionary
+        with open(temp_gtf.name, 'a+') as tmp:
+            with open(self.input_gtf_false_path, 'r') as gtf:
+                lines = gtf.readlines()
+                for index, line in enumerate(lines):
+                    # If this is not a comment, we check the fields
+                    if not line.startswith('#'):
+                        fields = line.split()
+                        # We are interested in fields[0] => Seqname (scaffold)
+                        # We are interested in fields[3] => Start of the scaffold
+                        # We are interested in fields[4] => End of the scaffold
+                        scaffold_size = dict_chrom_sizes[fields[0]]
+                        start_position = fields[3]
+                        end_position = fields[4]
+
+                        if start_position > 0 and end_position <= scaffold_size:
+                            # We are good, so we copy this line
+                            tmp.write(line)
+                            tmp.write(os.linesep)
+
+
+                        # The sequence is not good, we are going to process it regarding the user choice
+                        # TODO: Process the user choice
+                        # By default, we are assuming the user choice is to remove the lines: We don't copy it
+
+                        # If we are here, it means the gtf has been modified
+                        else:
+                            # We save the line for the feedback to the user
+                            modified_gtf.array_modified_lines.append(index + 1)
+
+                            if modified_gtf.is_modified is False:
+                                modified_gtf.is_modified = True
+                            else:
+                                pass
+                    else:
+                        tmp.write(line)
+                        tmp.write(os.linesep)
+
+        # Once the process it completed, we just replace the path of the gtf
+        self.input_gtf_false_path = temp_gtf.name
+
+        # TODO: Manage the issue with the fact the dataset is going to still exist on the disk because of delete=False
+
+        return modified_gtf

diff -r 000000000000 -r f493979f1408 Gtf.pyc

Binary file Gtf.pyc has changed

diff -r 000000000000 -r f493979f1408 LICENSE.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE.txt Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,46 @@\n+Academic Free License ("AFL") v. 3.0\n+This Academic Free License (the "License") applies to any original work of authorship (the "Original Work") whose owner (the "Licensor") has placed the following licensing notice adjacent to the copyright notice for the Original Work:\n+\n+Licensed under the Academic Free License version 3.0\n+\n+1) Grant of Copyright License. Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license, for the duration of the copyright, to do the following:\n+\n+a) to reproduce the Original Work in copies, either alone or as part of a collective work;\n+\n+b) to translate, adapt, alter, transform, modify, or arrange the Original Work, thereby creating derivative works ("Derivative Works") based upon the Original Work;\n+\n+c) to distribute or communicate copies of the Original Work and Derivative Works to the public, under any license of your choice that does not contradict the terms and conditions, including Licensor\'s reserved rights and remedies, in this Academic Free License;\n+\n+d) to perform the Original Work publicly; and\n+\n+e) to display the Original Work publicly.\n+\n+2) Grant of Patent License. Licensor grants You a worldwide, royalty-free, non-exclusive, sublicensable license, under patent claims owned or controlled by the Licensor that are embodied in the Original Work as furnished by the Licensor, for the duration of the patents, to make, use, sell, offer for sale, have made, and import the Original Work and Derivative Works.\n+\n+3) Grant of Source Code License. The term "Source Code" means the preferred form of the Original Work for making modifications to it and all available documentation describing how to modify the Original Work. Licensor agrees to provide a machine-readable copy of the Source Code of the Original Work along with each copy of the Original Work that Licensor distributes. Licensor reserves the right to satisfy this obligation by placing a machine-readable copy of the Source Code in an information repository reasonably calculated to permit inexpensive and convenient access by You for as long as Licensor continues to distribute the Original Work.\n+\n+4) Exclusions From License Grant. Neither the names of Licensor, nor the names of any contributors to the Original Work, nor any of their trademarks or service marks, may be used to endorse or promote products derived from this Original Work without express prior permission of the Licensor. Except as expressly stated herein, nothing in this License grants any license to Licensor\'s trademarks, copyrights, patents, trade secrets or any other intellectual property. No patent license is granted to make, use, sell, offer for sale, have made, or import embodiments of any patent claims other than the licensed claims defined in Section 2. No license is granted to the trademarks of Licensor even if such marks are included in the Original Work. Nothing in this License shall be interpreted to prohibit Licensor from licensing under terms different from this License any Original Work that Licensor otherwise would have a right to license.\n+\n+5) External Deployment. The term "External Deployment" means the use, distribution, or communication of the Original Work or Derivative Works in any way such that the Original Work or Derivative Works may be used by anyone other than You, whether those works are distributed or communicated to those persons or made available as an application intended for use over a network. As an express condition for the grants of license hereunder, You must treat any External Deployment by You of the Original Work or a Derivative Work as a distribution under section 1(c).\n+\n+6) Attribution Rights. You must retain, in the Source Code of any Derivative Works that You create, all copyright, patent, or trademark notices from the Source Code of the Original Work, as well as any notices of licensing and any descriptive text identified therein as an "Attribution Notice." You must cause the Source C'..b'right exceptions and limitations (including "fair use" or "fair dealing"). This License shall terminate immediately and You may no longer exercise any of the rights granted to You by this License upon your failure to honor the conditions in Section 1(c).\n+\n+10) Termination for Patent Action. This License shall terminate automatically and You may no longer exercise any of the rights granted to You by this License as of the date You commence an action, including a cross-claim or counterclaim, against Licensor or any licensee alleging that the Original Work infringes a patent. This termination provision shall not apply for an action alleging patent infringement by combinations of the Original Work with other software or hardware.\n+\n+11) Jurisdiction, Venue and Governing Law. Any action or suit relating to this License may be brought only in the courts of a jurisdiction wherein the Licensor resides or in which Licensor conducts its primary business, and under the laws of that jurisdiction excluding its conflict-of-law provisions. The application of the United Nations Convention on Contracts for the International Sale of Goods is expressly excluded. Any use of the Original Work outside the scope of this License or after its termination shall be subject to the requirements and penalties of copyright or patent law in the appropriate jurisdiction. This section shall survive the termination of this License.\n+\n+12) Attorneys\' Fees. In any action to enforce the terms of this License or seeking damages relating thereto, the prevailing party shall be entitled to recover its costs and expenses, including, without limitation, reasonable attorneys\' fees and costs incurred in connection with such action, including any appeal of such action. This section shall survive the termination of this License.\n+\n+13) Miscellaneous. If any provision of this License is held to be unenforceable, such provision shall be reformed only to the extent necessary to make it enforceable.\n+\n+14) Definition of "You" in This License. "You" throughout this License, whether in upper or lower case, means an individual or a legal entity exercising rights under, and complying with all of the terms of, this License. For legal entities, "You" includes any entity that controls, is controlled by, or is under common control with you. For purposes of this definition, "control" means (i) the power, direct or indirect, to cause the direction or management of such entity, whether by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of the outstanding shares, or (iii) beneficial ownership of such entity.\n+\n+15) Right to Use. You may use the Original Work in all ways not otherwise restricted or conditioned by this License or by law, and Licensor promises not to interfere with or be responsible for such uses by You.\n+\n+16) Modification of This License. This License is Copyright \xc2\xa9 2005 Lawrence Rosen. Permission is granted to copy, distribute, or communicate this License without modification. Nothing in this License permits You to modify this License as applied to the Original Work or to Derivative Works. However, You may modify the text of this License and copy, distribute or communicate your modified version (the "Modified License") and apply it to other original works of authorship subject to the following conditions: (i) You may not indicate in any way that your Modified License is the "Academic Free License" or "AFL" and you may not use those names in the name of your Modified License; (ii) You must replace the notice specified in the first paragraph above with the notice "Licensed under <insert your license name here>" or with a notice of your own that is not confusingly similar to the notice in this License; and (iii) You may not claim that your original works are open source software unless your Modified License has been approved by Open Source Initiative (OSI) and You comply with its license review and certification process.\n\\ No newline at end of file\n'

diff -r 000000000000 -r f493979f1408 Psl.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Psl.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,60 @@
+import logging
+import os
+import tempfile
+
+# Internal dependencies
+from Datatype import Datatype
+from util import subtools
+
+
+class Psl(Datatype):
+    def __init__(self, input_psl_path, data_psl):
+        super(Psl, self).__init__()
+
+        self.track = None
+
+        self.input_psl_path = input_psl_path
+        self.name_psl = data_psl["name"]
+        self.priority = data_psl["order_index"]
+        self.track_color = data_psl["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_psl["group_name"]
+
+        # Temporary files
+        unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
+        sorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='psl')
+
+        # Get the bed12+12 with pslToBigPsl
+        subtools.pslToBigPsl(input_psl_path, unsorted_bed_formatted_psl_file.name)
+
+        # Sort the formatted psl into sorted_bed_formatted_psl_file
+        subtools.sort(unsorted_bed_formatted_psl_file.name, sorted_bed_formatted_psl_file.name)
+
+        # Get the binary indexed bigPsl with bedToBigBed
+        trackName = "".join((self.name_psl, ".bb"))
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
+
+        my_big_psl_file_path = os.path.join(self.myTrackFolderPath, trackName)
+
+        logging.debug("Hello")
+
+        with open(my_big_psl_file_path, 'w') as big_psl_file:
+            subtools.bedToBigBed(sorted_bed_formatted_psl_file.name,
+                                 self.chromSizesFile.name,
+                                 big_psl_file.name,
+                                 autoSql=auto_sql_option,
+                                 typeOption='bed12+12',
+                                 tab=True)
+
+        # Create the Track Object
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_psl,
+                         track_type='bigPsl', visibility='dense',
+                         priority=self.priority,
+                         track_file=my_big_psl_file_path,
+                         track_color=self.track_color,
+                         group_name=self.group_name)
+
+        print("- BigPsl %s created" % self.name_psl)
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 Psl.pyc

Binary file Psl.pyc has changed

diff -r 000000000000 -r f493979f1408 Track.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Track.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+#!/usr/bin/python
+
+# TODO: Is this still useful?
+class Track(object):
+    """Class to manage the track informations needed for Track Hub, in the TrackDb text file"""
+
+    def __init__(self, trackFile=None, trackDb=None):
+        self.trackFile = trackFile
+
+        self.trackDb = trackDb

diff -r 000000000000 -r f493979f1408 Track.pyc

Binary file Track.pyc has changed

diff -r 000000000000 -r f493979f1408 TrackDb.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TrackDb.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,19 @@
+#!/usr/bin/python
+
+class TrackDb(object):
+    """docstring for TrackDb"""
+
+    def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", visibility="",
+                 thickDrawItem='off', priority="0", track_color="#000000", group_name="Default"):
+        super(TrackDb, self).__init__()
+
+        self.trackName = trackName
+        self.longLabel = longLabel
+        self.shortLabel = shortLabel
+        self.trackDataURL = trackDataURL
+        self.trackType = trackType
+        self.visibility = visibility
+        self.thickDrawItem = thickDrawItem
+        self.priority = priority
+        self.track_color = track_color
+        self.group_name = group_name

diff -r 000000000000 -r f493979f1408 TrackDb.pyc

Binary file TrackDb.pyc has changed

diff -r 000000000000 -r f493979f1408 TrackHub.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TrackHub.py Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,329 @@\n+#!/usr/bin/python\n+# -*- coding: utf8 -*-\n+\n+import logging\n+import os\n+import tempfile\n+import shutil\n+import zipfile\n+\n+# Internal dependencies\n+from Datatype import Datatype\n+from util import subtools\n+\n+from mako.lookup import TemplateLookup\n+\n+\n+class TrackHub(object):\n+ """docstring for TrackHub"""\n+\n+ def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):\n+ super(TrackHub, self).__init__()\n+\n+ self.rootAssemblyHub = None\n+\n+ self.mySpecieFolderPath = None\n+ self.myTracksFolderPath = None\n+ self.tool_directory = tool_directory\n+\n+ self.reference_genome = inputFastaFile\n+ # TODO: Add the specie name\n+ self.genome_name = inputFastaFile.assembly_id\n+ self.specie_html = self.genome_name + \'.html\'\n+ self.default_pos = None\n+ self.user_email = user_email\n+\n+ # Set containing the groups already added. Updated by addGroup()\n+ self.groups = set()\n+\n+ # TODO: Modify according to the files passed in parameter\n+ # ---- Templates ----\n+ # Template trackDb\n+ mylookup = TemplateLookup(directories=[os.path.join(tool_directory, \'templates/trackDb\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ self.trackDbTemplate = mylookup.get_template("layout.txt")\n+\n+ # Template groups\n+ mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, \'templates/groupsTxt\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ self.groupsTemplate = mylookup.get_template("layout.txt")\n+\n+ # ---- End Templates ----\n+\n+ self.extra_files_path = extra_files_path\n+ self.outputFile = outputFile\n+\n+ # Create the structure of the Assembly Hub\n+ # TODO: Merge the following processing into a function as it is also used in twoBitCreator\n+ self.twoBitName = None\n+ self.two_bit_final_path = None\n+ self.chromSizesFile = None\n+\n+ self.default_pos = None\n+\n+ # Set all the missing variables of this class, and create physically the folders/files\n+ self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)\n+\n+ # Init the Datatype\n+ Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,\n+ self.extra_files_path, self.tool_directory,\n+ self.mySpecieFolderPath, self.myTracksFolderPath)\n+\n+ def createZip(self):\n+ for root, dirs, files in os.walk(self.rootAssemblyHub):\n+ # Get all files and construct the dir at the same time\n+ for file in files:\n+ self.outputZip.write(os.path.join(root, file))\n+\n+ self.outputZip.close()\n+\n+ def addTrack(self, trackDbObject=None):\n+ # Create the trackDb.txt file in the specie folder, if not exists\n+ # Else append the new track\n+ # TODO: Get this out of the function\n+ trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, \'trackDb.txt\')\n+\n+ # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object\n+ with open(trackDbTxtFilePath, \'a+\') as trackDbFile:\n+ trackDbs = [trackDbObject]\n+\n+ # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label\n+ # Add the group as well, if exists in trackDbObject\n+ self.addGroup(trackDbObject.group_name)\n+\n+ htmlMakoRendered = self.trackDbTemplate.render(\n+ trackDbs=trackDbs\n+ )\n+ trackDbFile.write(htmlMakoRendered)\n+\n+ logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName,\n+ trackDbObject.group_name.lower().replace(\' \', \'_\')))\n+\n+ def addGroup(self, group_name="'..b'rackDbPath=os.path.join(self.genome_name, "trackDb.txt"),\n+ groupsPath=os.path.join(self.genome_name, "groups.txt"),\n+ genomeDescription=self.genome_name,\n+ twoBitPath=twoBitPath,\n+ organismName=self.genome_name,\n+ defaultPosition=self.default_pos,\n+ orderKey="4500",\n+ scientificName=self.genome_name,\n+ pathAssemblyHtmlDescription=os.path.join(self.genome_name, "description.html")\n+ )\n+ genomesTxtFile.write(htmlMakoRendered)\n+\n+ def __fillHubTxt__(self, hubTxtFilePath):\n+ # TODO: Think about the inputs and outputs\n+ # TODO: Manage the template of this file\n+ mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, \'templates/hubTxt\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ mytemplate = mylookup.get_template(\'layout.txt\')\n+ with open(hubTxtFilePath, \'w\') as genomesTxtFile:\n+ # Write the content of the file genomes.txt\n+ htmlMakoRendered = mytemplate.render(\n+ hubName=(\'\'.join([\'gonramp\', self.genome_name.title()])),\n+ shortLabel=self.genome_name,\n+ longLabel=self.genome_name,\n+ genomesFile=\'genomes.txt\',\n+ email=self.user_email,\n+ descriptionUrl=self.specie_html\n+ )\n+ genomesTxtFile.write(htmlMakoRendered)\n+\n+ def __fillHubHtmlFile__(self, hubHtmlFilePath):\n+ # TODO: Think about the inputs and outputs\n+ # TODO: Manage the template of this file\n+ # renderer = pystache.Renderer(search_dirs="templates/hubDescription")\n+ # t = Template(templates.hubDescription.layout.html)\n+ mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, \'templates/hubDescription\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ mytemplate = mylookup.get_template("layout.txt")\n+ with open(hubHtmlFilePath, \'w\') as hubHtmlFile:\n+ htmlMakoRendered = mytemplate.render(\n+ specie=\'Dbia\',\n+ toolUsed=\'Augustus\',\n+ ncbiSpecieUrl=\'http://www.ncbi.nlm.nih.gov/genome/3499\',\n+ genomeID=\'3499\',\n+ specieFullName=\'Drosophila biarmipes\'\n+ )\n+ #hubHtmlFile.write(htmlMakoRendered)\n+\n+ def __fillDescriptionHtmlFile__(self, descriptionHtmlFilePath):\n+ # TODO: Think about the inputs and outputs\n+ # TODO: Manage the template of this file\n+ mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, \'templates/specieDescription\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ mytemplate = mylookup.get_template("layout.txt")\n+ with open(descriptionHtmlFilePath, \'w\') as descriptionHtmlFile:\n+ # Write the content of the file genomes.txt\n+ htmlMakoRendered = mytemplate.render(\n+ specieDescription=\'This is the description of the dbia\',\n+ )\n+ #descriptionHtmlFile.write(htmlMakoRendered)\n+\n+ def __fillGroupsTxtFile__(self, groupsTxtFilePath):\n+ # TODO: Reenable this function at some point\n+ mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, \'templates/groupsTxt\')],\n+ output_encoding=\'utf-8\', encoding_errors=\'replace\')\n+ mytemplate = mylookup.get_template("layout.txt")\n+ with open(groupsTxtFilePath, \'w\') as groupsTxtFile:\n+ # Write the content of groups.txt\n+ # groupsTxtFile.write(\'name map\')\n+ htmlMakoRendered = mytemplate.render(\n+ mapName=\'map\',\n+ labelMapping=\'Mapping\',\n+ prioriy=\'2\',\n+ isClosed=\'0\'\n+ )\n+ # groupsTxtFile.write(htmlMakoRendered)\n'

diff -r 000000000000 -r f493979f1408 TrackHub.pyc

Binary file TrackHub.pyc has changed

diff -r 000000000000 -r f493979f1408 __init__.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/__init__.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,19 @@
+# Set default logging handler to avoid "No handler found" warnings.
+import logging
+import sys
+
+try:  # Python 2.7+
+    from logging import NullHandler
+except ImportError:
+    class NullHandler(logging.Handler):
+        def emit(self, record):
+            pass
+
+logging.getLogger(__name__).addHandler(NullHandler())
+
+log_stdout = None
+log_stderr = None
+
+
+# TODO: Handle the Exception by dispatching the error depending on the (debug) mode
+#class Exception(Exception):
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 bigGenePred.as
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bigGenePred.as Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,25 @@
+table bigGenePred
+"bigGenePred gene models"
+   (
+   string chrom;       "Reference sequence chromosome or scaffold"
+   uint   chromStart;  "Start position in chromosome"
+   uint   chromEnd;    "End position in chromosome"
+   string name;        "Name or ID of item, ideally both human readable and unique"
+   uint score;         "Score (0-1000)"
+   char[1] strand;     "+ or - for strand"
+   uint thickStart;    "Start of where display should be thick (start codon)"
+   uint thickEnd;      "End of where display should be thick (stop codon)"
+   uint reserved;       "RGB value (use R,G,B string in input file)"
+   int blockCount;     "Number of blocks"
+   int[blockCount] blockSizes; "Comma separated list of block sizes"
+   int[blockCount] chromStarts; "Start positions relative to chromStart"
+   string name2;       "Alternative/human readable name"
+   string cdsStartStat; "Status of CDS start annotation (none, unknown, incomplete, or complete)"
+   string cdsEndStat;   "Status of CDS end annotation (none, unknown, incomplete, or complete)"
+   int[blockCount] exonFrames; "Exon frame {0,1,2}, or -1 if no frame for exon"
+   string type;        "Transcript type"
+   string geneName;    "Primary identifier for gene"
+   string geneName2;   "Alternative/human readable gene name"
+   string geneType;    "Gene type"
+   )
+

diff -r 000000000000 -r f493979f1408 bigPsl.as
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bigPsl.as Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,33 @@
+table bigPsl
+"bigPsl pairwise alignment"
+    (
+    string chrom;       "Reference sequence chromosome or scaffold"
+    uint   chromStart;  "Start position in chromosome"
+    uint   chromEnd;    "End position in chromosome"
+    string name;        "Name or ID of item, ideally both human readable and unique"
+    uint score;         "Score (0-1000)"
+    char[1] strand;     "+ or - for strand"
+    uint thickStart;    "Start of where display should be thick (start codon)"
+    uint thickEnd;      "End of where display should be thick (stop codon)"
+    uint reserved;       "RGB value (use R,G,B string in input file)"
+    int blockCount;     "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+
+    uint    oChromStart;"Start position in other chromosome"
+    uint    oChromEnd;  "End position in other chromosome"
+    char[1] oStrand;    "+ or - for other strand"
+    uint    oChromSize; "Size of other chromosome."
+    int[blockCount] oChromStarts; "Start positions relative to oChromStart"
+
+    lstring  oSequence;  "Sequence on other chrom (or edit list, or empty)"
+    string   oCDS;       "CDS in NCBI format"
+
+    uint    chromSize;"Size of target chromosome"
+
+    uint match;        "Number of bases matched."
+    uint misMatch; " Number of bases that don't match "
+    uint repMatch; " Number of bases that match but are part of repeats "
+    uint nCount;   " Number of 'N' bases "
+    )
+

diff -r 000000000000 -r f493979f1408 doc/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/Makefile Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,216 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo "  html       to make standalone HTML files"
+ @echo "  dirhtml    to make HTML files named index.html in directories"
+ @echo "  singlehtml to make a single large HTML file"
+ @echo "  pickle     to make pickle files"
+ @echo "  json       to make JSON files"
+ @echo "  htmlhelp   to make HTML files and a HTML help project"
+ @echo "  qthelp     to make HTML files and a qthelp project"
+ @echo "  applehelp  to make an Apple Help Book"
+ @echo "  devhelp    to make HTML files and a Devhelp project"
+ @echo "  epub       to make an epub"
+ @echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+ @echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+ @echo "  text       to make text files"
+ @echo "  man        to make manual pages"
+ @echo "  texinfo    to make Texinfo files"
+ @echo "  info       to make Texinfo files and run them through makeinfo"
+ @echo "  gettext    to make PO message catalogs"
+ @echo "  changes    to make an overview of all changed/added/deprecated items"
+ @echo "  xml        to make Docutils-native XML files"
+ @echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+ @echo "  linkcheck  to check all external links for integrity"
+ @echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+ @echo "  coverage   to run coverage check of the documentation (if enabled)"
+
+.PHONY: clean
+clean:
+ rm -rf $(BUILDDIR)/*
+
+.PHONY: html
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: dirhtml
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+.PHONY: singlehtml
+singlehtml:
+ $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+ @echo
+ @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+.PHONY: pickle
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+.PHONY: json
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+.PHONY: htmlhelp
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+       ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+.PHONY: qthelp
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+       ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+ @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/HubArchiveCreator.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/HubArchiveCreator.qhc"
+
+.PHONY: applehelp
+applehelp:
+ $(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+ @echo
+ @echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+ @echo "N.B. You won't be able to view it unless you put it in" \
+       "~/Library/Documentation/Help or install it in your application" \
+       "bundle."
+
+.PHONY: devhelp
+devhelp:
+ $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+ @echo
+ @echo "Build finished."
+ @echo "To view the help file:"
+ @echo "# mkdir -p $$HOME/.local/share/devhelp/HubArchiveCreator"
+ @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/HubArchiveCreator"
+ @echo "# devhelp"
+
+.PHONY: epub
+epub:
+ $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+ @echo
+ @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+.PHONY: latex
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+ @echo "Run \`make' in that directory to run these through (pdf)latex" \
+       "(use \`make latexpdf' here to do that automatically)."
+
+.PHONY: latexpdf
+latexpdf:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through pdflatex..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: latexpdfja
+latexpdfja:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+ @echo "Running LaTeX files through platex and dvipdfmx..."
+ $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+ @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+.PHONY: text
+text:
+ $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+ @echo
+ @echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+.PHONY: man
+man:
+ $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+ @echo
+ @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+.PHONY: texinfo
+texinfo:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo
+ @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+ @echo "Run \`make' in that directory to run these through makeinfo" \
+       "(use \`make info' here to do that automatically)."
+
+.PHONY: info
+info:
+ $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+ @echo "Running Texinfo files through makeinfo..."
+ make -C $(BUILDDIR)/texinfo info
+ @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+.PHONY: gettext
+gettext:
+ $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+ @echo
+ @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+.PHONY: changes
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+ @echo
+ @echo "The overview file is in $(BUILDDIR)/changes."
+
+.PHONY: linkcheck
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+       "or in $(BUILDDIR)/linkcheck/output.txt."
+
+.PHONY: doctest
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+       "results in $(BUILDDIR)/doctest/output.txt."
+
+.PHONY: coverage
+coverage:
+ $(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
+ @echo "Testing of coverage in the sources finished, look at the " \
+       "results in $(BUILDDIR)/coverage/python.txt."
+
+.PHONY: xml
+xml:
+ $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+ @echo
+ @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+.PHONY: pseudoxml
+pseudoxml:
+ $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+ @echo
+ @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

diff -r 000000000000 -r f493979f1408 doc/_build/.buildinfo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/.buildinfo Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 3481d79a5d63af6a25633386bb8c7dcc
+tags: 645f666f9bcd5a90fca523b33c5a78b7

diff -r 000000000000 -r f493979f1408 doc/_build/.doctrees/doc/index.doctree

Binary file doc/_build/.doctrees/doc/index.doctree has changed

diff -r 000000000000 -r f493979f1408 doc/_build/.doctrees/environment.pickle

Binary file doc/_build/.doctrees/environment.pickle has changed

diff -r 000000000000 -r f493979f1408 doc/_build/.doctrees/index.doctree

Binary file doc/_build/.doctrees/index.doctree has changed

diff -r 000000000000 -r f493979f1408 doc/_build/doctrees/code.doctree

Binary file doc/_build/doctrees/code.doctree has changed

diff -r 000000000000 -r f493979f1408 doc/_build/doctrees/environment.pickle

Binary file doc/_build/doctrees/environment.pickle has changed

diff -r 000000000000 -r f493979f1408 doc/_build/doctrees/index.doctree

Binary file doc/_build/doctrees/index.doctree has changed

diff -r 000000000000 -r f493979f1408 doc/_build/html/.buildinfo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/.buildinfo Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 5f81f91fc7d70eea3315f0bb9103fea8
+tags: 645f666f9bcd5a90fca523b33c5a78b7

diff -r 000000000000 -r f493979f1408 doc/_build/html/_modules/hubArchiveCreator.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_modules/hubArchiveCreator.html Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,400 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"\n+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n+\n+\n+<html xmlns="http://www.w3.org/1999/xhtml">\n+ <head>\n+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n+ \n+ <title>hubArchiveCreator — HubArchiveCreator 2.3 documentation</title>\n+ \n+ <link rel="stylesheet" href="../_static/classic.css" type="text/css" />\n+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />\n+ \n+ <script type="text/javascript">\n+ var DOCUMENTATION_OPTIONS = {\n+ URL_ROOT: \'../\',\n+ VERSION: \'2.3\',\n+ COLLAPSE_INDEX: false,\n+ FILE_SUFFIX: \'.html\',\n+ HAS_SOURCE: true\n+ };\n+ </script>\n+ <script type="text/javascript" src="../_static/jquery.js"></script>\n+ <script type="text/javascript" src="../_static/underscore.js"></script>\n+ <script type="text/javascript" src="../_static/doctools.js"></script>\n+ <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>\n+ <link rel="index" title="Index" href="../genindex.html" />\n+ <link rel="search" title="Search" href="../search.html" />\n+ <link rel="top" title="HubArchiveCreator 2.3 documentation" href="../index.html" />\n+ <link rel="up" title="Module code" href="index.html" /> \n+ </head>\n+ <body role="document">\n+ <div class="related" role="navigation" aria-label="related navigation">\n+ <h3>Navigation</h3>\n+ <ul>\n+ <li class="right" style="margin-right: 10px">\n+ <a href="../genindex.html" title="General Index"\n+ accesskey="I">index</a></li>\n+ <li class="right" >\n+ <a href="../py-modindex.html" title="Python Module Index"\n+ >modules</a> |</li>\n+ <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li>\n+ <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> »</li> \n+ </ul>\n+ </div> \n+\n+ <div class="document">\n+ <div class="documentwrapper">\n+ <div class="bodywrapper">\n+ <div class="body" role="main">\n+ \n+ <h1>Source code for hubArchiveCreator</h1><div class="highlight"><pre>\n+<span></span><span class="ch">#!/usr/bin/python</span>\n+<span class="c1"># -*- coding: utf8 -*-</span>\n+\n+<span class="sd">"""</span>\n+<span class="sd">This Galaxy tool permits to prepare your files to be ready for</span>\n+<span class="sd">Assembly Hub visualization.</span>\n+<span class="sd">Program test arguments:</span>\n+<span class="sd">hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</span>\n+<span class="sd">"""</span>\n+\n+<span class="kn">import</span> <span class="nn">argparse</span>\n+<span class="kn">import</span> <span class="nn">collections</span>\n+<span class="kn">import</span> <span class="nn">json</span>\n+<span class="kn">import</span> <span class="nn">logging</span>\n+<span class="kn">import</span> <span class="nn">os</span>\n+<span class="kn">import</span> <span class="nn">sys</span>\n+\n+<span class="c1"># Internal dependencies</span>\n+<span class="kn">from</span> <span class="nn">Bam</span> <span class="k">import</span> <span class="n">Bam</span>\n+<span class="kn">from</span> <span class="nn">BedSimpleRepeats</span> <span class="k">import</span> <span class="n">BedSimpleRepeats</span>\n+<span class="kn">from</span> <span class="nn">Bed</span> <span class="k">import</span> <span class="n">Bed</span>\n+<span class="kn">from</span> <span class="nn">BigWig</span> <span class="k">import</span> <span class="n">BigWig</span>\n+<span class="kn">from</span> <span class="nn">util.Fasta</span> <span class="k">import</span> <span class="n">Fasta</span>\n+<span class="kn">from</span> <span class="nn">util.Filters</span> <span class="k">import</span> '..b'span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span></div>\n+\n+<div class="viewcode-block" id="configure_logger_stderr"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_stderr">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_stderr</span><span class="p">():</span>\n+ <span class="sd">"""</span>\n+<span class="sd"> Configure what should be logged in stderr</span>\n+<span class="sd"> """</span>\n+ <span class="n">log_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span>\n+ <span class="n">log_error</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">ERROR</span><span class="p">)</span>\n+ <span class="n">log_error_format</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span>\n+\n+ <span class="n">formatter_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">log_error_format</span><span class="p">)</span>\n+\n+ <span class="n">log_error</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter_error</span><span class="p">)</span>\n+\n+ <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_error</span><span class="p">)</span></div>\n+\n+<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>\n+ <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="n">__name__</span><span class="p">)</span>\n+ <span class="n">main</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span>\n+</pre></div>\n+\n+ </div>\n+ </div>\n+ </div>\n+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">\n+ <div class="sphinxsidebarwrapper">\n+<div id="searchbox" style="display: none" role="search">\n+ <h3>Quick search</h3>\n+ <form class="search" action="../search.html" method="get">\n+ <div><input type="text" name="q" /></div>\n+ <div><input type="submit" value="Go" /></div>\n+ <input type="hidden" name="check_keywords" value="yes" />\n+ <input type="hidden" name="area" value="default" />\n+ </form>\n+</div>\n+<script type="text/javascript">$(\'#searchbox\').show(0);</script>\n+ </div>\n+ </div>\n+ <div class="clearer"></div>\n+ </div>\n+ <div class="related" role="navigation" aria-label="related navigation">\n+ <h3>Navigation</h3>\n+ <ul>\n+ <li class="right" style="margin-right: 10px">\n+ <a href="../genindex.html" title="General Index"\n+ >index</a></li>\n+ <li class="right" >\n+ <a href="../py-modindex.html" title="Python Module Index"\n+ >modules</a> |</li>\n+ <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li>\n+ <li class="nav-item nav-item-1"><a href="index.html" >Module code</a> »</li> \n+ </ul>\n+ </div>\n+ <div class="footer" role="contentinfo">\n+ © Copyright 2016, Remi Marenco.\n+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.\n+ </div>\n+ </body>\n+</html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/_modules/index.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_modules/index.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,90 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+    <title>Overview: module code — HubArchiveCreator 2.3 documentation</title>
+
+    <link rel="stylesheet" href="../_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    '../',
+        VERSION:     '2.3',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="../_static/jquery.js"></script>
+    <script type="text/javascript" src="../_static/underscore.js"></script>
+    <script type="text/javascript" src="../_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="top" title="HubArchiveCreator 2.3 documentation" href="../index.html" />
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="hubArchiveCreator.html">hubArchiveCreator</a></li>
+</ul>
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="../search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        © Copyright 2016, Remi Marenco.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
+    </div>
+  </body>
+</html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/_sources/code.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_sources/code.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+Auto Generated Documentation
+============================
+
+.. automodule:: hubArchiveCreator
+ :members:

diff -r 000000000000 -r f493979f1408 doc/_build/html/_sources/index.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_sources/index.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,22 @@
+.. HubArchiveCreator documentation master file, created by
+   sphinx-quickstart on Thu Nov  3 11:43:14 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to HubArchiveCreator's documentation!
+=============================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   code
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/ajax-loader.gif

Binary file doc/_build/html/_static/ajax-loader.gif has changed

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/basic.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/basic.css Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,611 @@\n+/*\n+ * basic.css\n+ * ~~~~~~~~~\n+ *\n+ * Sphinx stylesheet -- basic theme.\n+ *\n+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.\n+ * :license: BSD, see LICENSE for details.\n+ *\n+ */\n+\n+/* -- main layout ----------------------------------------------------------- */\n+\n+div.clearer {\n+ clear: both;\n+}\n+\n+/* -- relbar ---------------------------------------------------------------- */\n+\n+div.related {\n+ width: 100%;\n+ font-size: 90%;\n+}\n+\n+div.related h3 {\n+ display: none;\n+}\n+\n+div.related ul {\n+ margin: 0;\n+ padding: 0 0 0 10px;\n+ list-style: none;\n+}\n+\n+div.related li {\n+ display: inline;\n+}\n+\n+div.related li.right {\n+ float: right;\n+ margin-right: 5px;\n+}\n+\n+/* -- sidebar --------------------------------------------------------------- */\n+\n+div.sphinxsidebarwrapper {\n+ padding: 10px 5px 0 10px;\n+}\n+\n+div.sphinxsidebar {\n+ float: left;\n+ width: 230px;\n+ margin-left: -100%;\n+ font-size: 90%;\n+ word-wrap: break-word;\n+ overflow-wrap : break-word;\n+}\n+\n+div.sphinxsidebar ul {\n+ list-style: none;\n+}\n+\n+div.sphinxsidebar ul ul,\n+div.sphinxsidebar ul.want-points {\n+ margin-left: 20px;\n+ list-style: square;\n+}\n+\n+div.sphinxsidebar ul ul {\n+ margin-top: 0;\n+ margin-bottom: 0;\n+}\n+\n+div.sphinxsidebar form {\n+ margin-top: 10px;\n+}\n+\n+div.sphinxsidebar input {\n+ border: 1px solid #98dbcc;\n+ font-family: sans-serif;\n+ font-size: 1em;\n+}\n+\n+div.sphinxsidebar #searchbox input[type="text"] {\n+ width: 170px;\n+}\n+\n+img {\n+ border: 0;\n+ max-width: 100%;\n+}\n+\n+/* -- search page ----------------------------------------------------------- */\n+\n+ul.search {\n+ margin: 10px 0 0 20px;\n+ padding: 0;\n+}\n+\n+ul.search li {\n+ padding: 5px 0 5px 20px;\n+ background-image: url(file.png);\n+ background-repeat: no-repeat;\n+ background-position: 0 7px;\n+}\n+\n+ul.search li a {\n+ font-weight: bold;\n+}\n+\n+ul.search li div.context {\n+ color: #888;\n+ margin: 2px 0 0 30px;\n+ text-align: left;\n+}\n+\n+ul.keywordmatches li.goodmatch a {\n+ font-weight: bold;\n+}\n+\n+/* -- index page ------------------------------------------------------------ */\n+\n+table.contentstable {\n+ width: 90%;\n+}\n+\n+table.contentstable p.biglink {\n+ line-height: 150%;\n+}\n+\n+a.biglink {\n+ font-size: 1.3em;\n+}\n+\n+span.linkdescr {\n+ font-style: italic;\n+ padding-top: 5px;\n+ font-size: 90%;\n+}\n+\n+/* -- general index --------------------------------------------------------- */\n+\n+table.indextable {\n+ width: 100%;\n+}\n+\n+table.indextable td {\n+ text-align: left;\n+ vertical-align: top;\n+}\n+\n+table.indextable dl, table.indextable dd {\n+ margin-top: 0;\n+ margin-bottom: 0;\n+}\n+\n+table.indextable tr.pcap {\n+ height: 10px;\n+}\n+\n+table.indextable tr.cap {\n+ margin-top: 10px;\n+ background-color: #f2f2f2;\n+}\n+\n+img.toggler {\n+ margin-right: 3px;\n+ margin-top: 3px;\n+ cursor: pointer;\n+}\n+\n+div.modindex-jumpbox {\n+ border-top: 1px solid #ddd;\n+ border-bottom: 1px solid #ddd;\n+ margin: 1em 0 1em 0;\n+ padding: 0.4em;\n+}\n+\n+div.genindex-jumpbox {\n+ border-top: 1px solid #ddd;\n+ border-bottom: 1px solid #ddd;\n+ margin: 1em 0 1em 0;\n+ padding: 0.4em;\n+}\n+\n+/* -- general body styles --------------------------------------------------- */\n+\n+div.body p, div.body dd, div.body li, div.body blockquote {\n+ -moz-hyphens: auto;\n+ -ms-hyphens: auto;\n+ -webkit-hyphens: auto;\n+ hyphens: auto;\n+}\n+\n+a.headerlink {\n+ visibility: hidden;\n+}\n+\n+h1:hover > a.headerlink,\n+h2:hover > a.headerlink,\n+h3:hover > a.headerlink,\n+h4:hover > a.headerlink,\n+h5:hover > a.headerlink,\n+h6:hover > a.headerlink,\n+dt:hover > a.headerlink,\n+caption:hover > a.headerlink,\n+p.caption:hover > a.headerlink,\n+div.code-block-caption:hover > a.headerlink {\n+ visibility: visible;\n+}\n+\n+div.body p.caption {\n+ text-align: inherit;\n+}\n+\n+div.body td {\n+ text-align: left;\n+}\n+\n+.field-list ul {\n+ padding-left: 1em;\n+}'..b'bottom: none;\n+}\n+\n+/* -- figures --------------------------------------------------------------- */\n+\n+div.figure {\n+ margin: 0.5em;\n+ padding: 0.5em;\n+}\n+\n+div.figure p.caption {\n+ padding: 0.3em;\n+}\n+\n+div.figure p.caption span.caption-number {\n+ font-style: italic;\n+}\n+\n+div.figure p.caption span.caption-text {\n+}\n+\n+\n+/* -- other body styles ----------------------------------------------------- */\n+\n+ol.arabic {\n+ list-style: decimal;\n+}\n+\n+ol.loweralpha {\n+ list-style: lower-alpha;\n+}\n+\n+ol.upperalpha {\n+ list-style: upper-alpha;\n+}\n+\n+ol.lowerroman {\n+ list-style: lower-roman;\n+}\n+\n+ol.upperroman {\n+ list-style: upper-roman;\n+}\n+\n+dl {\n+ margin-bottom: 15px;\n+}\n+\n+dd p {\n+ margin-top: 0px;\n+}\n+\n+dd ul, dd table {\n+ margin-bottom: 10px;\n+}\n+\n+dd {\n+ margin-top: 3px;\n+ margin-bottom: 10px;\n+ margin-left: 30px;\n+}\n+\n+dt:target, .highlighted {\n+ background-color: #fbe54e;\n+}\n+\n+dl.glossary dt {\n+ font-weight: bold;\n+ font-size: 1.1em;\n+}\n+\n+.field-list ul {\n+ margin: 0;\n+ padding-left: 1em;\n+}\n+\n+.field-list p {\n+ margin: 0;\n+}\n+\n+.optional {\n+ font-size: 1.3em;\n+}\n+\n+.sig-paren {\n+ font-size: larger;\n+}\n+\n+.versionmodified {\n+ font-style: italic;\n+}\n+\n+.system-message {\n+ background-color: #fda;\n+ padding: 5px;\n+ border: 3px solid red;\n+}\n+\n+.footnote:target {\n+ background-color: #ffa;\n+}\n+\n+.line-block {\n+ display: block;\n+ margin-top: 1em;\n+ margin-bottom: 1em;\n+}\n+\n+.line-block .line-block {\n+ margin-top: 0;\n+ margin-bottom: 0;\n+ margin-left: 1.5em;\n+}\n+\n+.guilabel, .menuselection {\n+ font-family: sans-serif;\n+}\n+\n+.accelerator {\n+ text-decoration: underline;\n+}\n+\n+.classifier {\n+ font-style: oblique;\n+}\n+\n+abbr, acronym {\n+ border-bottom: dotted 1px;\n+ cursor: help;\n+}\n+\n+/* -- code displays --------------------------------------------------------- */\n+\n+pre {\n+ overflow: auto;\n+ overflow-y: hidden; /* fixes display issues on Chrome browsers */\n+}\n+\n+span.pre {\n+ -moz-hyphens: none;\n+ -ms-hyphens: none;\n+ -webkit-hyphens: none;\n+ hyphens: none;\n+}\n+\n+td.linenos pre {\n+ padding: 5px 0px;\n+ border: 0;\n+ background-color: transparent;\n+ color: #aaa;\n+}\n+\n+table.highlighttable {\n+ margin-left: 0.5em;\n+}\n+\n+table.highlighttable td {\n+ padding: 0 0.5em 0 0.5em;\n+}\n+\n+div.code-block-caption {\n+ padding: 2px 5px;\n+ font-size: small;\n+}\n+\n+div.code-block-caption code {\n+ background-color: transparent;\n+}\n+\n+div.code-block-caption + div > div.highlight > pre {\n+ margin-top: 0;\n+}\n+\n+div.code-block-caption span.caption-number {\n+ padding: 0.1em 0.3em;\n+ font-style: italic;\n+}\n+\n+div.code-block-caption span.caption-text {\n+}\n+\n+div.literal-block-wrapper {\n+ padding: 1em 1em 0;\n+}\n+\n+div.literal-block-wrapper div.highlight {\n+ margin: 0;\n+}\n+\n+code.descname {\n+ background-color: transparent;\n+ font-weight: bold;\n+ font-size: 1.2em;\n+}\n+\n+code.descclassname {\n+ background-color: transparent;\n+}\n+\n+code.xref, a code {\n+ background-color: transparent;\n+ font-weight: bold;\n+}\n+\n+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {\n+ background-color: transparent;\n+}\n+\n+.viewcode-link {\n+ float: right;\n+}\n+\n+.viewcode-back {\n+ float: right;\n+ font-family: sans-serif;\n+}\n+\n+div.viewcode-block:target {\n+ margin: -1px -10px;\n+ padding: 0 10px;\n+}\n+\n+/* -- math display ---------------------------------------------------------- */\n+\n+img.math {\n+ vertical-align: middle;\n+}\n+\n+div.body div.math p {\n+ text-align: center;\n+}\n+\n+span.eqno {\n+ float: right;\n+}\n+\n+/* -- printout stylesheet --------------------------------------------------- */\n+\n+@media print {\n+ div.document,\n+ div.documentwrapper,\n+ div.bodywrapper {\n+ margin: 0 !important;\n+ width: 100%;\n+ }\n+\n+ div.sphinxsidebar,\n+ div.related,\n+ div.footer,\n+ #top-link {\n+ display: none;\n+ }\n+}\n\\ No newline at end of file\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/classic.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/classic.css Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,261 @@
+/*
+ * default.css_t
+ * ~~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- default theme.
+ *
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: sans-serif;
+    font-size: 100%;
+    background-color: #11303d;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+div.document {
+    background-color: #1c4e63;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 230px;
+}
+
+div.body {
+    background-color: #ffffff;
+    color: #000000;
+    padding: 0 20px 30px 20px;
+}
+
+div.footer {
+    color: #ffffff;
+    width: 100%;
+    padding: 9px 0 9px 0;
+    text-align: center;
+    font-size: 75%;
+}
+
+div.footer a {
+    color: #ffffff;
+    text-decoration: underline;
+}
+
+div.related {
+    background-color: #133f52;
+    line-height: 30px;
+    color: #ffffff;
+}
+
+div.related a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar {
+}
+
+div.sphinxsidebar h3 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.4em;
+    font-weight: normal;
+    margin: 0;
+    padding: 0;
+}
+
+div.sphinxsidebar h3 a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar h4 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.3em;
+    font-weight: normal;
+    margin: 5px 0 0 0;
+    padding: 0;
+}
+
+div.sphinxsidebar p {
+    color: #ffffff;
+}
+
+div.sphinxsidebar p.topless {
+    margin: 5px 10px 10px 10px;
+}
+
+div.sphinxsidebar ul {
+    margin: 10px;
+    padding: 0;
+    color: #ffffff;
+}
+
+div.sphinxsidebar a {
+    color: #98dbcc;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+
+
+/* -- hyperlink styles ------------------------------------------------------ */
+
+a {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:visited {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:hover {
+    text-decoration: underline;
+}
+
+
+
+/* -- body styles ----------------------------------------------------------- */
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+    font-family: 'Trebuchet MS', sans-serif;
+    background-color: #f2f2f2;
+    font-weight: normal;
+    color: #20435c;
+    border-bottom: 1px solid #ccc;
+    margin: 20px -20px 10px -20px;
+    padding: 3px 0 3px 10px;
+}
+
+div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h2 { font-size: 160%; }
+div.body h3 { font-size: 140%; }
+div.body h4 { font-size: 120%; }
+div.body h5 { font-size: 110%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+    color: #c60f0f;
+    font-size: 0.8em;
+    padding: 0 4px 0 4px;
+    text-decoration: none;
+}
+
+a.headerlink:hover {
+    background-color: #c60f0f;
+    color: white;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+    text-align: justify;
+    line-height: 130%;
+}
+
+div.admonition p.admonition-title + p {
+    display: inline;
+}
+
+div.admonition p {
+    margin-bottom: 5px;
+}
+
+div.admonition pre {
+    margin-bottom: 5px;
+}
+
+div.admonition ul, div.admonition ol {
+    margin-bottom: 5px;
+}
+
+div.note {
+    background-color: #eee;
+    border: 1px solid #ccc;
+}
+
+div.seealso {
+    background-color: #ffc;
+    border: 1px solid #ff6;
+}
+
+div.topic {
+    background-color: #eee;
+}
+
+div.warning {
+    background-color: #ffe4e4;
+    border: 1px solid #f66;
+}
+
+p.admonition-title {
+    display: inline;
+}
+
+p.admonition-title:after {
+    content: ":";
+}
+
+pre {
+    padding: 5px;
+    background-color: #eeffcc;
+    color: #333333;
+    line-height: 120%;
+    border: 1px solid #ac9;
+    border-left: none;
+    border-right: none;
+}
+
+code {
+    background-color: #ecf0f3;
+    padding: 0 1px 0 1px;
+    font-size: 0.95em;
+}
+
+th {
+    background-color: #ede;
+}
+
+.warning code {
+    background: #efc2c2;
+}
+
+.note code {
+    background: #d6d6d6;
+}
+
+.viewcode-back {
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
+
+div.code-block-caption {
+    color: #efefef;
+    background-color: #1c4e63;
+}
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/comment-bright.png

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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/comment-close.png

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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/comment.png

Binary file doc/_build/html/_static/comment.png has changed

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/doctools.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/doctools.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,287 @@\n+/*\n+ * doctools.js\n+ * ~~~~~~~~~~~\n+ *\n+ * Sphinx JavaScript utilities for all documentation.\n+ *\n+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.\n+ * :license: BSD, see LICENSE for details.\n+ *\n+ */\n+\n+/**\n+ * select a different prefix for underscore\n+ */\n+$u = _.noConflict();\n+\n+/**\n+ * make the code below compatible with browsers without\n+ * an installed firebug like debugger\n+if (!window.console || !console.firebug) {\n+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir",\n+ "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",\n+ "profile", "profileEnd"];\n+ window.console = {};\n+ for (var i = 0; i < names.length; ++i)\n+ window.console[names[i]] = function() {};\n+}\n+ */\n+\n+/**\n+ * small helper function to urldecode strings\n+ */\n+jQuery.urldecode = function(x) {\n+ return decodeURIComponent(x).replace(/\\+/g, \' \');\n+};\n+\n+/**\n+ * small helper function to urlencode strings\n+ */\n+jQuery.urlencode = encodeURIComponent;\n+\n+/**\n+ * This function returns the parsed url parameters of the\n+ * current request. Multiple values per key are supported,\n+ * it will always return arrays of strings for the value parts.\n+ */\n+jQuery.getQueryParameters = function(s) {\n+ if (typeof s == \'undefined\')\n+ s = document.location.search;\n+ var parts = s.substr(s.indexOf(\'?\') + 1).split(\'&\');\n+ var result = {};\n+ for (var i = 0; i < parts.length; i++) {\n+ var tmp = parts[i].split(\'=\', 2);\n+ var key = jQuery.urldecode(tmp[0]);\n+ var value = jQuery.urldecode(tmp[1]);\n+ if (key in result)\n+ result[key].push(value);\n+ else\n+ result[key] = [value];\n+ }\n+ return result;\n+};\n+\n+/**\n+ * highlight a given string on a jquery object by wrapping it in\n+ * span elements with the given class name.\n+ */\n+jQuery.fn.highlightText = function(text, className) {\n+ function highlight(node) {\n+ if (node.nodeType == 3) {\n+ var val = node.nodeValue;\n+ var pos = val.toLowerCase().indexOf(text);\n+ if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {\n+ var span = document.createElement("span");\n+ span.className = className;\n+ span.appendChild(document.createTextNode(val.substr(pos, text.length)));\n+ node.parentNode.insertBefore(span, node.parentNode.insertBefore(\n+ document.createTextNode(val.substr(pos + text.length)),\n+ node.nextSibling));\n+ node.nodeValue = val.substr(0, pos);\n+ }\n+ }\n+ else if (!jQuery(node).is("button, select, textarea")) {\n+ jQuery.each(node.childNodes, function() {\n+ highlight(this);\n+ });\n+ }\n+ }\n+ return this.each(function() {\n+ highlight(this);\n+ });\n+};\n+\n+/*\n+ * backward compatibility for jQuery.browser\n+ * This will be supported until firefox bug is fixed.\n+ */\n+if (!jQuery.browser) {\n+ jQuery.uaMatch = function(ua) {\n+ ua = ua.toLowerCase();\n+\n+ var match = /(chrome)[ \\/]([\\w.]+)/.exec(ua) ||\n+ /(webkit)[ \\/]([\\w.]+)/.exec(ua) ||\n+ /(opera)(?:.*version|)[ \\/]([\\w.]+)/.exec(ua) ||\n+ /(msie) ([\\w.]+)/.exec(ua) ||\n+ ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\\w.]+)|)/.exec(ua) ||\n+ [];\n+\n+ return {\n+ browser: match[ 1 ] || "",\n+ version: match[ 2 ] || "0"\n+ };\n+ };\n+ jQuery.browser = {};\n+ jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;\n+}\n+\n+/**\n+ * Small JavaScript module for the documentation.\n+ */\n+var Documentation = {\n+\n+ init : function() {\n+ this.fixFirefoxAnchorBug();\n+ this.highlightSearchWords();\n+ this.initIndexTable();\n+ \n+ },\n+\n+ /**\n+ * i18n support\n+ */\n+ TRANSLATIONS : {},\n+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },\n+ LOCALE : \'unknown\',\n+\n+ // gettext and ngettext don\'t access this so that the functions\n+ // can safely bound to a different name (_ = Documentation.gettext)\n+ gettext : function(string) {\n+ var translated = Documentation.TRANSLATIONS[string];\n+ if (typeof translate'..b'es[key];\n+ this.PLURAL_EXPR = new Function(\'n\', \'return +(\' + catalog.plural_expr + \')\');\n+ this.LOCALE = catalog.locale;\n+ },\n+\n+ /**\n+ * add context elements like header anchor links\n+ */\n+ addContextElements : function() {\n+ $(\'div[id] > :header:first\').each(function() {\n+ $(\'<a class="headerlink">\\u00B6</a>\').\n+ attr(\'href\', \'#\' + this.id).\n+ attr(\'title\', _(\'Permalink to this headline\')).\n+ appendTo(this);\n+ });\n+ $(\'dt[id]\').each(function() {\n+ $(\'<a class="headerlink">\\u00B6</a>\').\n+ attr(\'href\', \'#\' + this.id).\n+ attr(\'title\', _(\'Permalink to this definition\')).\n+ appendTo(this);\n+ });\n+ },\n+\n+ /**\n+ * workaround a firefox stupidity\n+ * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075\n+ */\n+ fixFirefoxAnchorBug : function() {\n+ if (document.location.hash)\n+ window.setTimeout(function() {\n+ document.location.href += \'\';\n+ }, 10);\n+ },\n+\n+ /**\n+ * highlight the search words provided in the url in the text\n+ */\n+ highlightSearchWords : function() {\n+ var params = $.getQueryParameters();\n+ var terms = (params.highlight) ? params.highlight[0].split(/\\s+/) : [];\n+ if (terms.length) {\n+ var body = $(\'div.body\');\n+ if (!body.length) {\n+ body = $(\'body\');\n+ }\n+ window.setTimeout(function() {\n+ $.each(terms, function() {\n+ body.highlightText(this.toLowerCase(), \'highlighted\');\n+ });\n+ }, 10);\n+ $(\'<p class="highlight-link"><a href="javascript:Documentation.\' +\n+ \'hideSearchWords()">\' + _(\'Hide Search Matches\') + \'</a></p>\')\n+ .appendTo($(\'#searchbox\'));\n+ }\n+ },\n+\n+ /**\n+ * init the domain index toggle buttons\n+ */\n+ initIndexTable : function() {\n+ var togglers = $(\'img.toggler\').click(function() {\n+ var src = $(this).attr(\'src\');\n+ var idnum = $(this).attr(\'id\').substr(7);\n+ $(\'tr.cg-\' + idnum).toggle();\n+ if (src.substr(-9) == \'minus.png\')\n+ $(this).attr(\'src\', src.substr(0, src.length-9) + \'plus.png\');\n+ else\n+ $(this).attr(\'src\', src.substr(0, src.length-8) + \'minus.png\');\n+ }).css(\'display\', \'\');\n+ if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {\n+ togglers.click();\n+ }\n+ },\n+\n+ /**\n+ * helper function to hide the search marks again\n+ */\n+ hideSearchWords : function() {\n+ $(\'#searchbox .highlight-link\').fadeOut(300);\n+ $(\'span.highlighted\').removeClass(\'highlighted\');\n+ },\n+\n+ /**\n+ * make the url absolute\n+ */\n+ makeURL : function(relativeURL) {\n+ return DOCUMENTATION_OPTIONS.URL_ROOT + \'/\' + relativeURL;\n+ },\n+\n+ /**\n+ * get the current relative url\n+ */\n+ getCurrentURL : function() {\n+ var path = document.location.pathname;\n+ var parts = path.split(/\\//);\n+ $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\\//), function() {\n+ if (this == \'..\')\n+ parts.pop();\n+ });\n+ var url = parts.join(\'/\');\n+ return path.substring(url.lastIndexOf(\'/\') + 1, path.length - 1);\n+ },\n+\n+ initOnKeyListeners: function() {\n+ $(document).keyup(function(event) {\n+ var activeElementType = document.activeElement.tagName;\n+ // don\'t navigate when in search box or textarea\n+ if (activeElementType !== \'TEXTAREA\' && activeElementType !== \'INPUT\' && activeElementType !== \'SELECT\') {\n+ switch (event.keyCode) {\n+ case 37: // left\n+ var prevHref = $(\'link[rel="prev"]\').prop(\'href\');\n+ if (prevHref) {\n+ window.location.href = prevHref;\n+ return false;\n+ }\n+ case 39: // right\n+ var nextHref = $(\'link[rel="next"]\').prop(\'href\');\n+ if (nextHref) {\n+ window.location.href = nextHref;\n+ return false;\n+ }\n+ }\n+ }\n+ });\n+ }\n+};\n+\n+// quick alias for translations\n+_ = Documentation.gettext;\n+\n+$(document).ready(function() {\n+ Documentation.init();\n+});\n\\ No newline at end of file\n'

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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/jquery-1.11.1.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/jquery-1.11.1.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,10308 @@\n+/*!\n+ * jQuery JavaScript Library v1.11.1\n+ * http://jquery.com/\n+ *\n+ * Includes Sizzle.js\n+ * http://sizzlejs.com/\n+ *\n+ * Copyright 2005, 2014 jQuery Foundation, Inc. and other contributors\n+ * Released under the MIT license\n+ * http://jquery.org/license\n+ *\n+ * Date: 2014-05-01T17:42Z\n+ */\n+\n+(function( global, factory ) {\n+\n+\tif ( typeof module === "object" && typeof module.exports === "object" ) {\n+\t\t// For CommonJS and CommonJS-like environments where a proper window is present,\n+\t\t// execute the factory and get jQuery\n+\t\t// For environments that do not inherently posses a window with a document\n+\t\t// (such as Node.js), expose a jQuery-making factory as module.exports\n+\t\t// This accentuates the need for the creation of a real window\n+\t\t// e.g. var jQuery = require("jquery")(window);\n+\t\t// See ticket #14549 for more info\n+\t\tmodule.exports = global.document ?\n+\t\t\tfactory( global, true ) :\n+\t\t\tfunction( w ) {\n+\t\t\t\tif ( !w.document ) {\n+\t\t\t\t\tthrow new Error( "jQuery requires a window with a document" );\n+\t\t\t\t}\n+\t\t\t\treturn factory( w );\n+\t\t\t};\n+\t} else {\n+\t\tfactory( global );\n+\t}\n+\n+// Pass this if window is not defined yet\n+}(typeof window !== "undefined" ? window : this, function( window, noGlobal ) {\n+\n+// Can\'t do this because several apps including ASP.NET trace\n+// the stack via arguments.caller.callee and Firefox dies if\n+// you try to trace through "use strict" call chains. (#13335)\n+// Support: Firefox 18+\n+//\n+\n+var deletedIds = [];\n+\n+var slice = deletedIds.slice;\n+\n+var concat = deletedIds.concat;\n+\n+var push = deletedIds.push;\n+\n+var indexOf = deletedIds.indexOf;\n+\n+var class2type = {};\n+\n+var toString = class2type.toString;\n+\n+var hasOwn = class2type.hasOwnProperty;\n+\n+var support = {};\n+\n+\n+\n+var\n+\tversion = "1.11.1",\n+\n+\t// Define a local copy of jQuery\n+\tjQuery = function( selector, context ) {\n+\t\t// The jQuery object is actually just the init constructor \'enhanced\'\n+\t\t// Need init if jQuery is called (just allow error to be thrown if not included)\n+\t\treturn new jQuery.fn.init( selector, context );\n+\t},\n+\n+\t// Support: Android<4.1, IE<9\n+\t// Make sure we trim BOM and NBSP\n+\trtrim = /^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,\n+\n+\t// Matches dashed string for camelizing\n+\trmsPrefix = /^-ms-/,\n+\trdashAlpha = /-([\\da-z])/gi,\n+\n+\t// Used by jQuery.camelCase as callback to replace()\n+\tfcamelCase = function( all, letter ) {\n+\t\treturn letter.toUpperCase();\n+\t};\n+\n+jQuery.fn = jQuery.prototype = {\n+\t// The current version of jQuery being used\n+\tjquery: version,\n+\n+\tconstructor: jQuery,\n+\n+\t// Start with an empty selector\n+\tselector: "",\n+\n+\t// The default length of a jQuery object is 0\n+\tlength: 0,\n+\n+\ttoArray: function() {\n+\t\treturn slice.call( this );\n+\t},\n+\n+\t// Get the Nth element in the matched element set OR\n+\t// Get the whole matched element set as a clean array\n+\tget: function( num ) {\n+\t\treturn num != null ?\n+\n+\t\t\t// Return just the one element from the set\n+\t\t\t( num < 0 ? this[ num + this.length ] : this[ num ] ) :\n+\n+\t\t\t// Return all the elements in a clean array\n+\t\t\tslice.call( this );\n+\t},\n+\n+\t// Take an array of elements and push it onto the stack\n+\t// (returning the new matched element set)\n+\tpushStack: function( elems ) {\n+\n+\t\t// Build a new jQuery matched element set\n+\t\tvar ret = jQuery.merge( this.constructor(), elems );\n+\n+\t\t// Add the old object onto the stack (as a reference)\n+\t\tret.prevObject = this;\n+\t\tret.context = this.context;\n+\n+\t\t// Return the newly-formed element set\n+\t\treturn ret;\n+\t},\n+\n+\t// Execute a callback for every element in the matched set.\n+\t// (You can seed the arguments with an array of args, but this is\n+\t// only used internally.)\n+\teach: function( callback, args ) {\n+\t\treturn jQuery.each( this, callback, args );\n+\t},\n+\n+\tmap: function( callback ) {\n+\t\treturn this.pushStack( jQuery.map(this, function( elem, i ) {\n+\t\t\treturn callback.call( elem, i, elem );\n+\t\t}));\n+\t},\n+\n+\tslice: function() {\n+\t\treturn this.pushStack( slice.apply( this, arguments ) );\n+\t},\n+\n+\t'..b'r it here\n+jQuery.each( [ "top", "left" ], function( i, prop ) {\n+\tjQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,\n+\t\tfunction( elem, computed ) {\n+\t\t\tif ( computed ) {\n+\t\t\t\tcomputed = curCSS( elem, prop );\n+\t\t\t\t// if curCSS returns percentage, fallback to offset\n+\t\t\t\treturn rnumnonpx.test( computed ) ?\n+\t\t\t\t\tjQuery( elem ).position()[ prop ] + "px" :\n+\t\t\t\t\tcomputed;\n+\t\t\t}\n+\t\t}\n+\t);\n+});\n+\n+\n+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods\n+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {\n+\tjQuery.each( { padding: "inner" + name, content: type, "": "outer" + name }, function( defaultExtra, funcName ) {\n+\t\t// margin is only for outerHeight, outerWidth\n+\t\tjQuery.fn[ funcName ] = function( margin, value ) {\n+\t\t\tvar chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),\n+\t\t\t\textra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );\n+\n+\t\t\treturn access( this, function( elem, type, value ) {\n+\t\t\t\tvar doc;\n+\n+\t\t\t\tif ( jQuery.isWindow( elem ) ) {\n+\t\t\t\t\t// As of 5/8/2012 this will yield incorrect results for Mobile Safari, but there\n+\t\t\t\t\t// isn\'t a whole lot we can do. See pull request at this URL for discussion:\n+\t\t\t\t\t// https://github.com/jquery/jquery/pull/764\n+\t\t\t\t\treturn elem.document.documentElement[ "client" + name ];\n+\t\t\t\t}\n+\n+\t\t\t\t// Get document width or height\n+\t\t\t\tif ( elem.nodeType === 9 ) {\n+\t\t\t\t\tdoc = elem.documentElement;\n+\n+\t\t\t\t\t// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], whichever is greatest\n+\t\t\t\t\t// unfortunately, this causes bug #3838 in IE6/8 only, but there is currently no good, small way to fix it.\n+\t\t\t\t\treturn Math.max(\n+\t\t\t\t\t\telem.body[ "scroll" + name ], doc[ "scroll" + name ],\n+\t\t\t\t\t\telem.body[ "offset" + name ], doc[ "offset" + name ],\n+\t\t\t\t\t\tdoc[ "client" + name ]\n+\t\t\t\t\t);\n+\t\t\t\t}\n+\n+\t\t\t\treturn value === undefined ?\n+\t\t\t\t\t// Get width or height on the element, requesting but not forcing parseFloat\n+\t\t\t\t\tjQuery.css( elem, type, extra ) :\n+\n+\t\t\t\t\t// Set width or height on the element\n+\t\t\t\t\tjQuery.style( elem, type, value, extra );\n+\t\t\t}, type, chainable ? margin : undefined, chainable, null );\n+\t\t};\n+\t});\n+});\n+\n+\n+// The number of elements contained in the matched element set\n+jQuery.fn.size = function() {\n+\treturn this.length;\n+};\n+\n+jQuery.fn.andSelf = jQuery.fn.addBack;\n+\n+\n+\n+\n+// Register as a named AMD module, since jQuery can be concatenated with other\n+// files that may use define, but not via a proper concatenation script that\n+// understands anonymous AMD modules. A named AMD is safest and most robust\n+// way to register. Lowercase jquery is used because AMD module names are\n+// derived from file names, and jQuery is normally delivered in a lowercase\n+// file name. Do this after creating the global so that if an AMD module wants\n+// to call noConflict to hide this version of jQuery, it will work.\n+\n+// Note that for maximum portability, libraries that are not jQuery should\n+// declare themselves as anonymous modules, and avoid setting a global if an\n+// AMD loader is present. jQuery is a special case. For more information, see\n+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon\n+\n+if ( typeof define === "function" && define.amd ) {\n+\tdefine( "jquery", [], function() {\n+\t\treturn jQuery;\n+\t});\n+}\n+\n+\n+\n+\n+var\n+\t// Map over jQuery in case of overwrite\n+\t_jQuery = window.jQuery,\n+\n+\t// Map over the $ in case of overwrite\n+\t_$ = window.$;\n+\n+jQuery.noConflict = function( deep ) {\n+\tif ( window.$ === jQuery ) {\n+\t\twindow.$ = _$;\n+\t}\n+\n+\tif ( deep && window.jQuery === jQuery ) {\n+\t\twindow.jQuery = _jQuery;\n+\t}\n+\n+\treturn jQuery;\n+};\n+\n+// Expose jQuery and $ identifiers, even in\n+// AMD (#7102#comment:10, https://github.com/jquery/jquery/pull/557)\n+// and CommonJS for browser emulators (#13566)\n+if ( typeof noGlobal === strundefined ) {\n+\twindow.jQuery = window.$ = jQuery;\n+}\n+\n+\n+\n+\n+return jQuery;\n+\n+}));\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/jquery.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/jquery.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,4 @@\n+/*! jQuery v1.11.1 | (c) 2005, 2014 jQuery Foundation, Inc. | jquery.org/license */\n+!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=c.slice,e=c.concat,f=c.push,g=c.indexOf,h={},i=h.toString,j=h.hasOwnProperty,k={},l="1.11.1",m=function(a,b){return new m.fn.init(a,b)},n=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,o=/^-ms-/,p=/-([\\da-z])/gi,q=function(a,b){return b.toUpperCase()};m.fn=m.prototype={jquery:l,constructor:m,selector:"",length:0,toArray:function(){return d.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:d.call(this)},pushStack:function(a){var b=m.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a,b){return m.each(this,a,b)},map:function(a){return this.pushStack(m.map(this,function(b,c){return a.call(b,c,b)}))},slice:function(){return this.pushStack(d.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(a){var b=this.length,c=+a+(0>a?b:0);return this.pushStack(c>=0&&b>c?[this[c]]:[])},end:function(){return this.prevObject||this.constructor(null)},push:f,sort:c.sort,splice:c.splice},m.extend=m.fn.extend=function(){var a,b,c,d,e,f,g=arguments[0]||{},h=1,i=arguments.length,j=!1;for("boolean"==typeof g&&(j=g,g=arguments[h]||{},h++),"object"==typeof g||m.isFunction(g)||(g={}),h===i&&(g=this,h--);i>h;h++)if(null!=(e=arguments[h]))for(d in e)a=g[d],c=e[d],g!==c&&(j&&c&&(m.isPlainObject(c)||(b=m.isArray(c)))?(b?(b=!1,f=a&&m.isArray(a)?a:[]):f=a&&m.isPlainObject(a)?a:{},g[d]=m.extend(j,f,c)):void 0!==c&&(g[d]=c));return g},m.extend({expando:"jQuery"+(l+Math.random()).replace(/\\D/g,""),isReady:!0,error:function(a){throw new 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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/pygments.css
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/pygments.css Wed Dec 21 12:13:04 2016 -0500

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+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
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+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
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+.highlight .ge { font-style: italic } /* Generic.Emph */
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+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
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+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
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+.highlight .m { color: #208050 } /* Literal.Number */
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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/searchtools.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/searchtools.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,651 @@\n+/*\n+ * searchtools.js_t\n+ * ~~~~~~~~~~~~~~~~\n+ *\n+ * Sphinx JavaScript utilities for the full-text search.\n+ *\n+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.\n+ * :license: BSD, see LICENSE for details.\n+ *\n+ */\n+\n+\n+/* Non-minified version JS is _stemmer.js if file is provided */ \n+/**\n+ * Porter Stemmer\n+ */\n+var Stemmer = function() {\n+\n+ var step2list = {\n+ ational: \'ate\',\n+ tional: \'tion\',\n+ enci: \'ence\',\n+ anci: \'ance\',\n+ izer: \'ize\',\n+ bli: \'ble\',\n+ alli: \'al\',\n+ entli: \'ent\',\n+ eli: \'e\',\n+ ousli: \'ous\',\n+ ization: \'ize\',\n+ ation: \'ate\',\n+ ator: \'ate\',\n+ alism: \'al\',\n+ iveness: \'ive\',\n+ fulness: \'ful\',\n+ ousness: \'ous\',\n+ aliti: \'al\',\n+ iviti: \'ive\',\n+ biliti: \'ble\',\n+ logi: \'log\'\n+ };\n+\n+ var step3list = {\n+ icate: \'ic\',\n+ ative: \'\',\n+ alize: \'al\',\n+ iciti: \'ic\',\n+ ical: \'ic\',\n+ ful: \'\',\n+ ness: \'\'\n+ };\n+\n+ var c = "[^aeiou]"; // consonant\n+ var v = "[aeiouy]"; // vowel\n+ var C = c + "[^aeiouy]*"; // consonant sequence\n+ var V = v + "[aeiou]*"; // vowel sequence\n+\n+ var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0\n+ var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1\n+ var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1\n+ var s_v = "^(" + C + ")?" + v; // vowel in stem\n+\n+ this.stemWord = function (w) {\n+ var stem;\n+ var suffix;\n+ var firstch;\n+ var origword = w;\n+\n+ if (w.length < 3)\n+ return w;\n+\n+ var re;\n+ var re2;\n+ var re3;\n+ var re4;\n+\n+ firstch = w.substr(0,1);\n+ if (firstch == "y")\n+ w = firstch.toUpperCase() + w.substr(1);\n+\n+ // Step 1a\n+ re = /^(.+?)(ss|i)es$/;\n+ re2 = /^(.+?)([^s])s$/;\n+\n+ if (re.test(w))\n+ w = w.replace(re,"$1$2");\n+ else if (re2.test(w))\n+ w = w.replace(re2,"$1$2");\n+\n+ // Step 1b\n+ re = /^(.+?)eed$/;\n+ re2 = /^(.+?)(ed|ing)$/;\n+ if (re.test(w)) {\n+ var fp = re.exec(w);\n+ re = new RegExp(mgr0);\n+ if (re.test(fp[1])) {\n+ re = /.$/;\n+ w = w.replace(re,"");\n+ }\n+ }\n+ else if (re2.test(w)) {\n+ var fp = re2.exec(w);\n+ stem = fp[1];\n+ re2 = new RegExp(s_v);\n+ if (re2.test(stem)) {\n+ w = stem;\n+ re2 = /(at|bl|iz)$/;\n+ re3 = new RegExp("([^aeiouylsz])\\\\1$");\n+ re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");\n+ if (re2.test(w))\n+ w = w + "e";\n+ else if (re3.test(w)) {\n+ re = /.$/;\n+ w = w.replace(re,"");\n+ }\n+ else if (re4.test(w))\n+ w = w + "e";\n+ }\n+ }\n+\n+ // Step 1c\n+ re = /^(.+?)y$/;\n+ if (re.test(w)) {\n+ var fp = re.exec(w);\n+ stem = fp[1];\n+ re = new RegExp(s_v);\n+ if (re.test(stem))\n+ w = stem + "i";\n+ }\n+\n+ // Step 2\n+ re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n+ if (re.test(w)) {\n+ var fp = re.exec(w);\n+ stem = fp[1];\n+ suffix = fp[2];\n+ re = new RegExp(mgr0);\n+ if (re.test(stem))\n+ w = stem + step2list[suffix];\n+ }\n+\n+ // Step 3\n+ re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n+ if (re.test(w)) {\n+ var fp = re.exec(w);\n+ stem = fp[1];\n+ suffix = fp[2];\n+ re = new RegExp(mgr0);\n+ if (re.test(stem))\n+ w = stem + step3list[suffix];\n+ }\n+\n+ // Step 4\n+ re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n+ re2 = /^(.+?)(s|t)(ion)$/;\n+ if (re.test(w)) {\n+ var fp = re.exec(w);\n+ stem = fp[1];\n+ re = new RegExp(mgr1);\n+ if (re.test(stem))\n+ w = stem;\n+ }\n+ else if (re2.test(w)) {\n+ var fp = re2.exec(w);\n+ stem = fp[1] + fp[2];\n+ re2 = new RegExp(mgr1);\n+ if (re2.'..b' custom score for some objects according to scorer\n+ if (Scorer.objPrio.hasOwnProperty(match[2])) {\n+ score += Scorer.objPrio[match[2]];\n+ } else {\n+ score += Scorer.objPrioDefault;\n+ }\n+ results.push([filenames[match[0]], fullname, \'#\'+anchor, descr, score]);\n+ }\n+ }\n+ }\n+\n+ return results;\n+ },\n+\n+ /**\n+ * search for full-text terms in the index\n+ */\n+ performTermsSearch : function(searchterms, excluded, terms, titleterms) {\n+ var filenames = this._index.filenames;\n+ var titles = this._index.titles;\n+\n+ var i, j, file;\n+ var fileMap = {};\n+ var scoreMap = {};\n+ var results = [];\n+\n+ // perform the search on the required terms\n+ for (i = 0; i < searchterms.length; i++) {\n+ var word = searchterms[i];\n+ var files = [];\n+ var _o = [\n+ {files: terms[word], score: Scorer.term},\n+ {files: titleterms[word], score: Scorer.title}\n+ ];\n+\n+ // no match but word was a required one\n+ if ($u.every(_o, function(o){return o.files === undefined;})) {\n+ break;\n+ }\n+ // found search word in contents\n+ $u.each(_o, function(o) {\n+ var _files = o.files;\n+ if (_files === undefined)\n+ return\n+\n+ if (_files.length === undefined)\n+ _files = [_files];\n+ files = files.concat(_files);\n+\n+ // set score for the word in each file to Scorer.term\n+ for (j = 0; j < _files.length; j++) {\n+ file = _files[j];\n+ if (!(file in scoreMap))\n+ scoreMap[file] = {}\n+ scoreMap[file][word] = o.score;\n+ }\n+ });\n+\n+ // create the mapping\n+ for (j = 0; j < files.length; j++) {\n+ file = files[j];\n+ if (file in fileMap)\n+ fileMap[file].push(word);\n+ else\n+ fileMap[file] = [word];\n+ }\n+ }\n+\n+ // now check if the files don\'t contain excluded terms\n+ for (file in fileMap) {\n+ var valid = true;\n+\n+ // check if all requirements are matched\n+ if (fileMap[file].length != searchterms.length)\n+ continue;\n+\n+ // ensure that none of the excluded terms is in the search result\n+ for (i = 0; i < excluded.length; i++) {\n+ if (terms[excluded[i]] == file ||\n+ titleterms[excluded[i]] == file ||\n+ $u.contains(terms[excluded[i]] || [], file) ||\n+ $u.contains(titleterms[excluded[i]] || [], file)) {\n+ valid = false;\n+ break;\n+ }\n+ }\n+\n+ // if we have still a valid result we can add it to the result list\n+ if (valid) {\n+ // select one (max) score for the file.\n+ // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...\n+ var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));\n+ results.push([filenames[file], titles[file], \'\', null, score]);\n+ }\n+ }\n+ return results;\n+ },\n+\n+ /**\n+ * helper function to return a node containing the\n+ * search summary for a given text. keywords is a list\n+ * of stemmed words, hlwords is the list of normal, unstemmed\n+ * words. the first one is used to find the occurrence, the\n+ * latter for highlighting it.\n+ */\n+ makeSearchSummary : function(text, keywords, hlwords) {\n+ var textLower = text.toLowerCase();\n+ var start = 0;\n+ $.each(keywords, function() {\n+ var i = textLower.indexOf(this.toLowerCase());\n+ if (i > -1)\n+ start = i;\n+ });\n+ start = Math.max(start - 120, 0);\n+ var excerpt = ((start > 0) ? \'...\' : \'\') +\n+ $.trim(text.substr(start, 240)) +\n+ ((start + 240 - text.length) ? \'...\' : \'\');\n+ var rv = $(\'<div class="context"></div>\').text(excerpt);\n+ $.each(hlwords, function() {\n+ rv = rv.highlightText(this, \'highlighted\');\n+ });\n+ return rv;\n+ }\n+};\n+\n+$(document).ready(function() {\n+ Search.init();\n+});\n\\ No newline at end of file\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/sidebar.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/sidebar.js Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,159 @@
+/*
+ * sidebar.js
+ * ~~~~~~~~~~
+ *
+ * This script makes the Sphinx sidebar collapsible.
+ *
+ * .sphinxsidebar contains .sphinxsidebarwrapper.  This script adds
+ * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
+ * used to collapse and expand the sidebar.
+ *
+ * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
+ * and the width of the sidebar and the margin-left of the document
+ * are decreased. When the sidebar is expanded the opposite happens.
+ * This script saves a per-browser/per-session cookie used to
+ * remember the position of the sidebar among the pages.
+ * Once the browser is closed the cookie is deleted and the position
+ * reset to the default (expanded).
+ *
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+$(function() {
+
+
+
+
+
+
+
+
+  // global elements used by the functions.
+  // the 'sidebarbutton' element is defined as global after its
+  // creation, in the add_sidebar_button function
+  var bodywrapper = $('.bodywrapper');
+  var sidebar = $('.sphinxsidebar');
+  var sidebarwrapper = $('.sphinxsidebarwrapper');
+
+  // for some reason, the document has no sidebar; do not run into errors
+  if (!sidebar.length) return;
+
+  // original margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar expanded
+  var bw_margin_expanded = bodywrapper.css('margin-left');
+  var ssb_width_expanded = sidebar.width();
+
+  // margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar collapsed
+  var bw_margin_collapsed = '.8em';
+  var ssb_width_collapsed = '.8em';
+
+  // colors used by the current theme
+  var dark_color = $('.related').css('background-color');
+  var light_color = $('.document').css('background-color');
+
+  function sidebar_is_collapsed() {
+    return sidebarwrapper.is(':not(:visible)');
+  }
+
+  function toggle_sidebar() {
+    if (sidebar_is_collapsed())
+      expand_sidebar();
+    else
+      collapse_sidebar();
+  }
+
+  function collapse_sidebar() {
+    sidebarwrapper.hide();
+    sidebar.css('width', ssb_width_collapsed);
+    bodywrapper.css('margin-left', bw_margin_collapsed);
+    sidebarbutton.css({
+        'margin-left': '0',
+        'height': bodywrapper.height()
+    });
+    sidebarbutton.find('span').text('»');
+    sidebarbutton.attr('title', _('Expand sidebar'));
+    document.cookie = 'sidebar=collapsed';
+  }
+
+  function expand_sidebar() {
+    bodywrapper.css('margin-left', bw_margin_expanded);
+    sidebar.css('width', ssb_width_expanded);
+    sidebarwrapper.show();
+    sidebarbutton.css({
+        'margin-left': ssb_width_expanded-12,
+        'height': bodywrapper.height()
+    });
+    sidebarbutton.find('span').text('«');
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    document.cookie = 'sidebar=expanded';
+  }
+
+  function add_sidebar_button() {
+    sidebarwrapper.css({
+        'float': 'left',
+        'margin-right': '0',
+        'width': ssb_width_expanded - 28
+    });
+    // create the button
+    sidebar.append(
+        '<div id="sidebarbutton"><span>«</span></div>'
+    );
+    var sidebarbutton = $('#sidebarbutton');
+    light_color = sidebarbutton.css('background-color');
+    // find the height of the viewport to center the '<<' in the page
+    var viewport_height;
+    if (window.innerHeight)
+   viewport_height = window.innerHeight;
+    else
+   viewport_height = $(window).height();
+    sidebarbutton.find('span').css({
+        'display': 'block',
+        'margin-top': (viewport_height - sidebar.position().top - 20) / 2
+    });
+
+    sidebarbutton.click(toggle_sidebar);
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    sidebarbutton.css({
+        'color': '#FFFFFF',
+        'border-left': '1px solid ' + dark_color,
+        'font-size': '1.2em',
+        'cursor': 'pointer',
+        'height': bodywrapper.height(),
+        'padding-top': '1px',
+        'margin-left': ssb_width_expanded - 12
+    });
+
+    sidebarbutton.hover(
+      function () {
+          $(this).css('background-color', dark_color);
+      },
+      function () {
+          $(this).css('background-color', light_color);
+      }
+    );
+  }
+
+  function set_position_from_cookie() {
+    if (!document.cookie)
+      return;
+    var items = document.cookie.split(';');
+    for(var k=0; k<items.length; k++) {
+      var key_val = items[k].split('=');
+      var key = key_val[0].replace(/ /, "");  // strip leading spaces
+      if (key == 'sidebar') {
+        var value = key_val[1];
+        if ((value == 'collapsed') && (!sidebar_is_collapsed()))
+          collapse_sidebar();
+        else if ((value == 'expanded') && (sidebar_is_collapsed()))
+          expand_sidebar();
+      }
+    }
+  }
+
+  add_sidebar_button();
+  var sidebarbutton = $('#sidebarbutton');
+  set_position_from_cookie();
+});
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/underscore-1.3.1.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/underscore-1.3.1.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,999 @@\n+// Underscore.js 1.3.1\n+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.\n+// Underscore is freely distributable under the MIT license.\n+// Portions of Underscore are inspired or borrowed from Prototype,\n+// Oliver Steele\'s Functional, and John Resig\'s Micro-Templating.\n+// For all details and documentation:\n+// http://documentcloud.github.com/underscore\n+\n+(function() {\n+\n+ // Baseline setup\n+ // --------------\n+\n+ // Establish the root object, `window` in the browser, or `global` on the server.\n+ var root = this;\n+\n+ // Save the previous value of the `_` variable.\n+ var previousUnderscore = root._;\n+\n+ // Establish the object that gets returned to break out of a loop iteration.\n+ var breaker = {};\n+\n+ // Save bytes in the minified (but not gzipped) version:\n+ var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;\n+\n+ // Create quick reference variables for speed access to core prototypes.\n+ var slice = ArrayProto.slice,\n+ unshift = ArrayProto.unshift,\n+ toString = ObjProto.toString,\n+ hasOwnProperty = ObjProto.hasOwnProperty;\n+\n+ // All **ECMAScript 5** native function implementations that we hope to use\n+ // are declared here.\n+ var\n+ nativeForEach = ArrayProto.forEach,\n+ nativeMap = ArrayProto.map,\n+ nativeReduce = ArrayProto.reduce,\n+ nativeReduceRight = ArrayProto.reduceRight,\n+ nativeFilter = ArrayProto.filter,\n+ nativeEvery = ArrayProto.every,\n+ nativeSome = ArrayProto.some,\n+ nativeIndexOf = ArrayProto.indexOf,\n+ nativeLastIndexOf = ArrayProto.lastIndexOf,\n+ nativeIsArray = Array.isArray,\n+ nativeKeys = Object.keys,\n+ nativeBind = FuncProto.bind;\n+\n+ // Create a safe reference to the Underscore object for use below.\n+ var _ = function(obj) { return new wrapper(obj); };\n+\n+ // Export the Underscore object for **Node.js**, with\n+ // backwards-compatibility for the old `require()` API. If we\'re in\n+ // the browser, add `_` as a global object via a string identifier,\n+ // for Closure Compiler "advanced" mode.\n+ if (typeof exports !== \'undefined\') {\n+ if (typeof module !== \'undefined\' && module.exports) {\n+ exports = module.exports = _;\n+ }\n+ exports._ = _;\n+ } else {\n+ root[\'_\'] = _;\n+ }\n+\n+ // Current version.\n+ _.VERSION = \'1.3.1\';\n+\n+ // Collection Functions\n+ // --------------------\n+\n+ // The cornerstone, an `each` implementation, aka `forEach`.\n+ // Handles objects with the built-in `forEach`, arrays, and raw objects.\n+ // Delegates to **ECMAScript 5**\'s native `forEach` if available.\n+ var each = _.each = _.forEach = function(obj, iterator, context) {\n+ if (obj == null) return;\n+ if (nativeForEach && obj.forEach === nativeForEach) {\n+ obj.forEach(iterator, context);\n+ } else if (obj.length === +obj.length) {\n+ for (var i = 0, l = obj.length; i < l; i++) {\n+ if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;\n+ }\n+ } else {\n+ for (var key in obj) {\n+ if (_.has(obj, key)) {\n+ if (iterator.call(context, obj[key], key, obj) === breaker) return;\n+ }\n+ }\n+ }\n+ };\n+\n+ // Return the results of applying the iterator to each element.\n+ // Delegates to **ECMAScript 5**\'s native `map` if available.\n+ _.map = _.collect = function(obj, iterator, context) {\n+ var results = [];\n+ if (obj == null) return results;\n+ if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);\n+ each(obj, function(value, index, list) {\n+ results[results.length] = iterator.call(context, value, index, list);\n+ });\n+ if (obj.length === +obj.length) results.length = obj.length;\n+ return results;\n+ };\n+\n+ // **Reduce** builds up a single result from a list of values, aka `inject`,\n+ // or `foldl`. Delegates to **ECMAScript 5**\'s nat'..b's, change the\n+ // following template settings to use alternative delimiters.\n+ _.templateSettings = {\n+ evaluate : /<%([\\s\\S]+?)%>/g,\n+ interpolate : /<%=([\\s\\S]+?)%>/g,\n+ escape : /<%-([\\s\\S]+?)%>/g\n+ };\n+\n+ // When customizing `templateSettings`, if you don\'t want to define an\n+ // interpolation, evaluation or escaping regex, we need one that is\n+ // guaranteed not to match.\n+ var noMatch = /.^/;\n+\n+ // Within an interpolation, evaluation, or escaping, remove HTML escaping\n+ // that had been previously added.\n+ var unescape = function(code) {\n+ return code.replace(/\\\\\\\\/g, \'\\\\\').replace(/\\\\\'/g, "\'");\n+ };\n+\n+ // JavaScript micro-templating, similar to John Resig\'s implementation.\n+ // Underscore templating handles arbitrary delimiters, preserves whitespace,\n+ // and correctly escapes quotes within interpolated code.\n+ _.template = function(str, data) {\n+ var c = _.templateSettings;\n+ var tmpl = \'var __p=[],print=function(){__p.push.apply(__p,arguments);};\' +\n+ \'with(obj||{}){__p.push(\\\'\' +\n+ str.replace(/\\\\/g, \'\\\\\\\\\')\n+ .replace(/\'/g, "\\\\\'")\n+ .replace(c.escape || noMatch, function(match, code) {\n+ return "\',_.escape(" + unescape(code) + "),\'";\n+ })\n+ .replace(c.interpolate || noMatch, function(match, code) {\n+ return "\'," + unescape(code) + ",\'";\n+ })\n+ .replace(c.evaluate || noMatch, function(match, code) {\n+ return "\');" + unescape(code).replace(/[\\r\\n\\t]/g, \' \') + ";__p.push(\'";\n+ })\n+ .replace(/\\r/g, \'\\\\r\')\n+ .replace(/\\n/g, \'\\\\n\')\n+ .replace(/\\t/g, \'\\\\t\')\n+ + "\');}return __p.join(\'\');";\n+ var func = new Function(\'obj\', \'_\', tmpl);\n+ if (data) return func(data, _);\n+ return function(data) {\n+ return func.call(this, data, _);\n+ };\n+ };\n+\n+ // Add a "chain" function, which will delegate to the wrapper.\n+ _.chain = function(obj) {\n+ return _(obj).chain();\n+ };\n+\n+ // The OOP Wrapper\n+ // ---------------\n+\n+ // If Underscore is called as a function, it returns a wrapped object that\n+ // can be used OO-style. This wrapper holds altered versions of all the\n+ // underscore functions. Wrapped objects may be chained.\n+ var wrapper = function(obj) { this._wrapped = obj; };\n+\n+ // Expose `wrapper.prototype` as `_.prototype`\n+ _.prototype = wrapper.prototype;\n+\n+ // Helper function to continue chaining intermediate results.\n+ var result = function(obj, chain) {\n+ return chain ? _(obj).chain() : obj;\n+ };\n+\n+ // A method to easily add functions to the OOP wrapper.\n+ var addToWrapper = function(name, func) {\n+ wrapper.prototype[name] = function() {\n+ var args = slice.call(arguments);\n+ unshift.call(args, this._wrapped);\n+ return result(func.apply(_, args), this._chain);\n+ };\n+ };\n+\n+ // Add all of the Underscore functions to the wrapper object.\n+ _.mixin(_);\n+\n+ // Add all mutator Array functions to the wrapper.\n+ each([\'pop\', \'push\', \'reverse\', \'shift\', \'sort\', \'splice\', \'unshift\'], function(name) {\n+ var method = ArrayProto[name];\n+ wrapper.prototype[name] = function() {\n+ var wrapped = this._wrapped;\n+ method.apply(wrapped, arguments);\n+ var length = wrapped.length;\n+ if ((name == \'shift\' || name == \'splice\') && length === 0) delete wrapped[0];\n+ return result(wrapped, this._chain);\n+ };\n+ });\n+\n+ // Add all accessor Array functions to the wrapper.\n+ each([\'concat\', \'join\', \'slice\'], function(name) {\n+ var method = ArrayProto[name];\n+ wrapper.prototype[name] = function() {\n+ return result(method.apply(this._wrapped, arguments), this._chain);\n+ };\n+ });\n+\n+ // Start chaining a wrapped Underscore object.\n+ wrapper.prototype.chain = function() {\n+ this._chain = true;\n+ return this;\n+ };\n+\n+ // Extracts the result from a wrapped and chained object.\n+ wrapper.prototype.value = function() {\n+ return this._wrapped;\n+ };\n+\n+}).call(this);\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/underscore.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/underscore.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,31 @@\n+// Underscore.js 1.3.1\n+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.\n+// Underscore is freely distributable under the MIT license.\n+// Portions of Underscore are inspired or borrowed from Prototype,\n+// Oliver Steele\'s Functional, and John Resig\'s Micro-Templating.\n+// For all details and documentation:\n+// http://documentcloud.github.com/underscore\n+(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==\n+c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c,\n+h)&&!f--)break;g=!f}}d.pop();return g}var r=this,G=r._,n={},k=Array.prototype,o=Object.prototype,i=k.slice,H=k.unshift,l=o.toString,I=o.hasOwnProperty,w=k.forEach,x=k.map,y=k.reduce,z=k.reduceRight,A=k.filter,B=k.every,C=k.some,p=k.indexOf,D=k.lastIndexOf,o=Array.isArray,J=Object.keys,s=Function.prototype.bind,b=function(a){return new m(a)};if(typeof exports!=="undefined"){if(typeof module!=="undefined"&&module.exports)exports=module.exports=b;exports._=b}else r._=b;b.VERSION="1.3.1";var j=b.each=\n+b.forEach=function(a,c,d){if(a!=null)if(w&&a.forEach===w)a.forEach(c,d);else if(a.length===+a.length)for(var e=0,f=a.length;e<f;e++){if(e in a&&c.call(d,a[e],e,a)===n)break}else for(e in a)if(b.has(a,e)&&c.call(d,a[e],e,a)===n)break};b.map=b.collect=function(a,c,b){var e=[];if(a==null)return e;if(x&&a.map===x)return a.map(c,b);j(a,function(a,g,h){e[e.length]=c.call(b,a,g,h)});if(a.length===+a.length)e.length=a.length;return e};b.reduce=b.foldl=b.inject=function(a,c,d,e){var f=arguments.length>2;a==\n+null&&(a=[]);if(y&&a.reduce===y)return e&&(c=b.bind(c,e)),f?a.reduce(c,d):a.reduce(c);j(a,function(a,b,i){f?d=c.call(e,d,a,b,i):(d=a,f=true)});if(!f)throw new TypeError("Reduce of empty array with no initial value");return d};b.reduceRight=b.foldr=function(a,c,d,e){var f=arguments.length>2;a==null&&(a=[]);if(z&&a.reduceRight===z)return e&&(c=b.bind(c,e)),f?a.reduceRight(c,d):a.reduceRight(c);var g=b.toArray(a).reverse();e&&!f&&(c=b.bind(c,e));return f?b.reduce(g,c,d,e):b.reduce(g,c)};b.find=b.detect=\n+function(a,c,b){var e;E(a,function(a,g,h){if(c.call(b,a,g,h))return e=a,true});return e};b.filter=b.select=function(a,c,b){var e=[];if(a==null)return e;if(A&&a.filter===A)return a.filter(c,b);j(a,function(a,g,h){c.call(b,a,g,h)&&(e[e.length]=a)});return e};b.reject=function(a,c,b){var e=[];if(a==null)return e;j(a,function(a,g,h){c.call(b,a,g,h)||(e[e.length]=a)});return e};b.every=b.all=function(a,c,b){var e=true;if(a==null)return e;if(B&&a.every===B)return a.every(c,b);j(a,function(a,g,h){if(!(e=\n+e&&c.call(b,a,g,h)))return n});return e};var E=b.some=b.any=function(a,c,d){c||(c=b.identity);var e=false;if(a==null)return e;if(C&&a.some===C)return a.some(c,d);j(a,function(a,b,h){if(e||(e=c.call(d,a,b,h)))return n});return!!e};b.include=b.contains=function(a,c){var b=false;if(a==null)return b;return p&&a.indexOf===p?a.indexOf(c)!=-1:b=E(a,function(a){return a===c})};b.invoke=function(a,c){var d=i.call(arguments,2);return 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Date]"};\n+b.isRegExp=function(a){return l.call(a)=="[object RegExp]"};b.isNull=function(a){return a===null};b.isUndefined=function(a){return a===void 0};b.has=function(a,b){return I.call(a,b)};b.noConflict=function(){r._=G;return this};b.identity=function(a){return a};b.times=function(a,b,d){for(var e=0;e<a;e++)b.call(d,e)};b.escape=function(a){return(""+a).replace(/&/g,"&").replace(/</g,"<").replace(/>/g,">").replace(/"/g,""").replace(/\'/g,"'").replace(/\\//g,"/")};b.mixin=function(a){j(b.functions(a),\n+function(c){K(c,b[c]=a[c])})};var L=0;b.uniqueId=function(a){var b=L++;return a?a+b:b};b.templateSettings={evaluate:/<%([\\s\\S]+?)%>/g,interpolate:/<%=([\\s\\S]+?)%>/g,escape:/<%-([\\s\\S]+?)%>/g};var t=/.^/,u=function(a){return a.replace(/\\\\\\\\/g,"\\\\").replace(/\\\\\'/g,"\'")};b.template=function(a,c){var d=b.templateSettings,d="var 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diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/up-pressed.png

Binary file doc/_build/html/_static/up-pressed.png has changed

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/up.png

Binary file doc/_build/html/_static/up.png has changed

diff -r 000000000000 -r f493979f1408 doc/_build/html/_static/websupport.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/websupport.js Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,808 @@\n+/*\n+ * websupport.js\n+ * ~~~~~~~~~~~~~\n+ *\n+ * sphinx.websupport utilities for all documentation.\n+ *\n+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.\n+ * :license: BSD, see LICENSE for details.\n+ *\n+ */\n+\n+(function($) {\n+ $.fn.autogrow = function() {\n+ return this.each(function() {\n+ var textarea = this;\n+\n+ $.fn.autogrow.resize(textarea);\n+\n+ $(textarea)\n+ .focus(function() {\n+ textarea.interval = setInterval(function() {\n+ $.fn.autogrow.resize(textarea);\n+ }, 500);\n+ })\n+ .blur(function() {\n+ clearInterval(textarea.interval);\n+ });\n+ });\n+ };\n+\n+ $.fn.autogrow.resize = function(textarea) {\n+ var lineHeight = parseInt($(textarea).css(\'line-height\'), 10);\n+ var lines = textarea.value.split(\'\\n\');\n+ var columns = textarea.cols;\n+ var lineCount = 0;\n+ $.each(lines, function() {\n+ lineCount += Math.ceil(this.length / columns) || 1;\n+ });\n+ var height = lineHeight * (lineCount + 1);\n+ $(textarea).css(\'height\', height);\n+ };\n+})(jQuery);\n+\n+(function($) {\n+ var comp, by;\n+\n+ function init() {\n+ initEvents();\n+ initComparator();\n+ }\n+\n+ function initEvents() {\n+ $(document).on("click", \'a.comment-close\', function(event) {\n+ event.preventDefault();\n+ hide($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.vote\', function(event) {\n+ event.preventDefault();\n+ handleVote($(this));\n+ });\n+ $(document).on("click", \'a.reply\', function(event) {\n+ event.preventDefault();\n+ openReply($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.close-reply\', function(event) {\n+ event.preventDefault();\n+ closeReply($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.sort-option\', function(event) {\n+ event.preventDefault();\n+ handleReSort($(this));\n+ });\n+ $(document).on("click", \'a.show-proposal\', function(event) {\n+ event.preventDefault();\n+ showProposal($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.hide-proposal\', function(event) {\n+ event.preventDefault();\n+ hideProposal($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.show-propose-change\', function(event) {\n+ event.preventDefault();\n+ showProposeChange($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.hide-propose-change\', function(event) {\n+ event.preventDefault();\n+ hideProposeChange($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.accept-comment\', function(event) {\n+ event.preventDefault();\n+ acceptComment($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.delete-comment\', function(event) {\n+ event.preventDefault();\n+ deleteComment($(this).attr(\'id\').substring(2));\n+ });\n+ $(document).on("click", \'a.comment-markup\', function(event) {\n+ event.preventDefault();\n+ toggleCommentMarkupBox($(this).attr(\'id\').substring(2));\n+ });\n+ }\n+\n+ /**\n+ * Set comp, which is a comparator function used for sorting and\n+ * inserting comments into the list.\n+ */\n+ function setComparator() {\n+ // If the first three letters are "asc", sort in ascending order\n+ // and remove the prefix.\n+ if (by.substring(0,3) == \'asc\') {\n+ var i = by.substring(3);\n+ comp = function(a, b) { return a[i] - b[i]; };\n+ } else {\n+ // Otherwise sort in descending order.\n+ comp = function(a, b) { return b[by] - a[by]; };\n+ }\n+\n+ // Reset link styles and format the selected sort option.\n+ $(\'a.sel\').attr(\'href\', \'#\').removeClass(\'sel\');\n+ $(\'a.by\' + by).removeAttr(\'href\').addClass(\'sel\');\n+ }\n+\n+ /**\n+ * Create a comp function. If the user has preferences stored in\n+ * the sortBy cookie, use those, otherwise use the default.\n+ */\n+ function initComparator() {\n+ by = \'rating\'; // Default to sort b'..b'+ code blocks: <code>::</code> and an indented block after blank line</div>\\\n+ <form method="post" id="cf<%id%>" class="comment-form" action="">\\\n+ <textarea name="comment" cols="80"></textarea>\\\n+ <p class="propose-button">\\\n+ <a href="#" id="pc<%id%>" class="show-propose-change">\\\n+ Propose a change ▹\\\n+ </a>\\\n+ <a href="#" id="hc<%id%>" class="hide-propose-change">\\\n+ Propose a change ▿\\\n+ </a>\\\n+ </p>\\\n+ <textarea name="proposal" id="pt<%id%>" cols="80"\\\n+ spellcheck="false"></textarea>\\\n+ <input type="submit" value="Add comment" />\\\n+ <input type="hidden" name="node" value="<%id%>" />\\\n+ <input type="hidden" name="parent" value="" />\\\n+ </form>\\\n+ </div>\\\n+ </div>\';\n+\n+ var commentTemplate = \'\\\n+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\\\n+ <div class="vote">\\\n+ <div class="arrow">\\\n+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\\\n+ <img src="<%upArrow%>" />\\\n+ </a>\\\n+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\\\n+ <img src="<%upArrowPressed%>" />\\\n+ </a>\\\n+ </div>\\\n+ <div class="arrow">\\\n+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\\\n+ <img src="<%downArrow%>" id="da<%id%>" />\\\n+ </a>\\\n+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\\\n+ <img src="<%downArrowPressed%>" />\\\n+ </a>\\\n+ </div>\\\n+ </div>\\\n+ <div class="comment-content">\\\n+ <p class="tagline comment">\\\n+ <span class="user-id"><%username%></span>\\\n+ <span class="rating"><%pretty_rating%></span>\\\n+ <span class="delta"><%time.delta%></span>\\\n+ </p>\\\n+ <div class="comment-text comment"><#text#></div>\\\n+ <p class="comment-opts comment">\\\n+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\\\n+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\\\n+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\\\n+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\\\n+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\\\n+ <span id="cm<%id%>" class="moderation hidden">\\\n+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\\\n+ </span>\\\n+ </p>\\\n+ <pre class="proposal" id="pr<%id%>">\\\n+<#proposal_diff#>\\\n+ </pre>\\\n+ <ul class="comment-children" id="cl<%id%>"></ul>\\\n+ </div>\\\n+ <div class="clearleft"></div>\\\n+ </div>\\\n+ </div>\';\n+\n+ var replyTemplate = \'\\\n+ <li>\\\n+ <div class="reply-div" id="rd<%id%>">\\\n+ <form id="rf<%id%>">\\\n+ <textarea name="comment" cols="80"></textarea>\\\n+ <input type="submit" value="Add reply" />\\\n+ <input type="button" value="Cancel" />\\\n+ <input type="hidden" name="parent" value="<%id%>" />\\\n+ <input type="hidden" name="node" value="" />\\\n+ </form>\\\n+ </div>\\\n+ </li>\';\n+\n+ $(document).ready(function() {\n+ init();\n+ });\n+})(jQuery);\n+\n+$(document).ready(function() {\n+ // add comment anchors for all paragraphs that are commentable\n+ $(\'.sphinx-has-comment\').comment();\n+\n+ // highlight search words in search results\n+ $("div.context").each(function() {\n+ var params = $.getQueryParameters();\n+ var terms = (params.q) ? params.q[0].split(/\\s+/) : [];\n+ var result = $(this);\n+ $.each(terms, function() {\n+ result.highlightText(this.toLowerCase(), \'highlighted\');\n+ });\n+ });\n+\n+ // directly open comment window if requested\n+ var anchor = document.location.hash;\n+ if (anchor.substring(0, 9) == \'#comment-\') {\n+ $(\'#ao\' + anchor.substring(9)).click();\n+ document.location.hash = \'#s\' + anchor.substring(9);\n+ }\n+});\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/code.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/code.html Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,227 @@\n+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"\n+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n+\n+\n+<html xmlns="http://www.w3.org/1999/xhtml">\n+ <head>\n+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n+ \n+ <title>Auto Generated Documentation — HubArchiveCreator 2.3 documentation</title>\n+ \n+ <link rel="stylesheet" href="_static/classic.css" type="text/css" />\n+ <link rel="stylesheet" href="_static/pygments.css" type="text/css" />\n+ \n+ <script type="text/javascript">\n+ var DOCUMENTATION_OPTIONS = {\n+ URL_ROOT: \'./\',\n+ VERSION: \'2.3\',\n+ COLLAPSE_INDEX: false,\n+ FILE_SUFFIX: \'.html\',\n+ HAS_SOURCE: true\n+ };\n+ </script>\n+ <script type="text/javascript" src="_static/jquery.js"></script>\n+ <script type="text/javascript" src="_static/underscore.js"></script>\n+ <script type="text/javascript" src="_static/doctools.js"></script>\n+ <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>\n+ <link rel="index" title="Index" href="genindex.html" />\n+ <link rel="search" title="Search" href="search.html" />\n+ <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" />\n+ <link rel="prev" title="Welcome to HubArchiveCreator\xe2\x80\x99s documentation!" href="index.html" /> \n+ </head>\n+ <body role="document">\n+ <div class="related" role="navigation" aria-label="related navigation">\n+ <h3>Navigation</h3>\n+ <ul>\n+ <li class="right" style="margin-right: 10px">\n+ <a href="genindex.html" title="General Index"\n+ accesskey="I">index</a></li>\n+ <li class="right" >\n+ <a href="py-modindex.html" title="Python Module Index"\n+ >modules</a> |</li>\n+ <li class="right" >\n+ <a href="index.html" title="Welcome to HubArchiveCreator\xe2\x80\x99s documentation!"\n+ accesskey="P">previous</a> |</li>\n+ <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li> \n+ </ul>\n+ </div> \n+\n+ <div class="document">\n+ <div class="documentwrapper">\n+ <div class="bodywrapper">\n+ <div class="body" role="main">\n+ \n+ <div class="section" id="module-hubArchiveCreator">\n+<span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-hubArchiveCreator" title="Permalink to this headline">\xc2\xb6</a></h1>\n+<p>This Galaxy tool permits to prepare your files to be ready for\n+Assembly Hub visualization.\n+Program test arguments:\n+hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</p>\n+<dl class="function">\n+<dt id="hubArchiveCreator.configure_logger_dev">\n+<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_dev</code><span class="sig-paren">(</span><em>log_stdout=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_dev"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_dev" title="Permalink to this definition">\xc2\xb6</a></dt>\n+<dd><dl class="docutils">\n+<dt>Dev Logger is defined as following:</dt>\n+<dd><ul class="first last simple">\n+<li>Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</li>\n+<li>Still access to full, brute and traceback in stderr for errors</li>\n+<li>And further access to debug if needed</li>\n+</ul>\n+</dd>\n+</dl>\n+</dd></dl>\n+\n+<dl class="function">\n+<dt id="hubArchiveCreator.configure_logger_stderr">\n+<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_stderr</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiv'..b'class="field-body" />\n+<tbody valign="top">\n+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>string_to_sanitize</strong> – </td>\n+</tr>\n+</tbody>\n+</table>\n+<p>:return :</p>\n+<table class="docutils field-list" frame="void" rules="none">\n+<col class="field-name" />\n+<col class="field-body" />\n+<tbody valign="top">\n+<tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body"></td>\n+</tr>\n+</tbody>\n+</table>\n+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sanitize_name_input</span><span class="p">(</span><span class="s1">'this/is an//example'</span><span class="p">)</span>\n+<span class="go">this_is_an__example</span>\n+</pre></div>\n+</div>\n+</dd></dl>\n+\n+<dl class="function">\n+<dt id="hubArchiveCreator.sanitize_name_inputs">\n+<code class="descclassname">hubArchiveCreator.</code><code class="descname">sanitize_name_inputs</code><span class="sig-paren">(</span><em>inputs_data</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#sanitize_name_inputs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.sanitize_name_inputs" title="Permalink to this definition">\xc2\xb6</a></dt>\n+<dd><p>Sanitize value of the keys “name” of the dictionary passed in parameter.</p>\n+<p>Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.\n+Also, it can contain ‘/’ character and could break the use of os.path function.</p>\n+<table class="docutils field-list" frame="void" rules="none">\n+<col class="field-name" />\n+<col class="field-body" />\n+<tbody valign="top">\n+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>inputs_data</strong> – dict[string, dict[string, string]]</td>\n+</tr>\n+</tbody>\n+</table>\n+</dd></dl>\n+\n+</div>\n+\n+\n+ </div>\n+ </div>\n+ </div>\n+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">\n+ <div class="sphinxsidebarwrapper">\n+ <h4>Previous topic</h4>\n+ <p class="topless"><a href="index.html"\n+ title="previous chapter">Welcome to HubArchiveCreator’s documentation!</a></p>\n+ <div role="note" aria-label="source link">\n+ <h3>This Page</h3>\n+ <ul class="this-page-menu">\n+ <li><a href="_sources/code.txt"\n+ rel="nofollow">Show Source</a></li>\n+ </ul>\n+ </div>\n+<div id="searchbox" style="display: none" role="search">\n+ <h3>Quick search</h3>\n+ <form class="search" action="search.html" method="get">\n+ <div><input type="text" name="q" /></div>\n+ <div><input type="submit" value="Go" /></div>\n+ <input type="hidden" name="check_keywords" value="yes" />\n+ <input type="hidden" name="area" value="default" />\n+ </form>\n+</div>\n+<script type="text/javascript">$(\'#searchbox\').show(0);</script>\n+ </div>\n+ </div>\n+ <div class="clearer"></div>\n+ </div>\n+ <div class="related" role="navigation" aria-label="related navigation">\n+ <h3>Navigation</h3>\n+ <ul>\n+ <li class="right" style="margin-right: 10px">\n+ <a href="genindex.html" title="General Index"\n+ >index</a></li>\n+ <li class="right" >\n+ <a href="py-modindex.html" title="Python Module Index"\n+ >modules</a> |</li>\n+ <li class="right" >\n+ <a href="index.html" title="Welcome to HubArchiveCreator\xe2\x80\x99s documentation!"\n+ >previous</a> |</li>\n+ <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li> \n+ </ul>\n+ </div>\n+ <div class="footer" role="contentinfo">\n+ © Copyright 2016, Remi Marenco.\n+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.\n+ </div>\n+ </body>\n+</html>\n\\ No newline at end of file\n'

diff -r 000000000000 -r f493979f1408 doc/_build/html/genindex.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/genindex.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,151 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+    <title>Index — HubArchiveCreator 2.3 documentation</title>
+
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '2.3',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="index" title="Index" href="#" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" />
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#C"><strong>C</strong></a>
+ | <a href="#H"><strong>H</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+
+</div>
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="code.html#hubArchiveCreator.configure_logger_dev">configure_logger_dev() (in module hubArchiveCreator)</a>
+  </dt>
+
+
+  <dt><a href="code.html#hubArchiveCreator.configure_logger_stderr">configure_logger_stderr() (in module hubArchiveCreator)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="code.html#hubArchiveCreator.configure_logger_user">configure_logger_user() (in module hubArchiveCreator)</a>
+  </dt>
+
+
+  <dt><a href="code.html#hubArchiveCreator.create_ordered_datatype_objects">create_ordered_datatype_objects() (in module hubArchiveCreator)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="code.html#module-hubArchiveCreator">hubArchiveCreator (module)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="code.html#hubArchiveCreator.sanitize_name_input">sanitize_name_input() (in module hubArchiveCreator)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+
+  <dt><a href="code.html#hubArchiveCreator.sanitize_name_inputs">sanitize_name_inputs() (in module hubArchiveCreator)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+
+
+
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="#" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        © Copyright 2016, Remi Marenco.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
+    </div>
+  </body>
+</html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/index.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/index.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,128 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+    <title>Welcome to HubArchiveCreator’s documentation! — HubArchiveCreator 2.3 documentation</title>
+
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '2.3',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="top" title="HubArchiveCreator 2.3 documentation" href="#" />
+    <link rel="next" title="Auto Generated Documentation" href="code.html" />
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="code.html" title="Auto Generated Documentation"
+             accesskey="N">next</a> |</li>
+        <li class="nav-item nav-item-0"><a href="#">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <div class="section" id="welcome-to-hubarchivecreator-s-documentation">
+<h1>Welcome to HubArchiveCreator’s documentation!<a class="headerlink" href="#welcome-to-hubarchivecreator-s-documentation" title="Permalink to this headline">¶</a></h1>
+<p>Contents:</p>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="code.html">Auto Generated Documentation</a></li>
+</ul>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
+<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
+</ul>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+  <h3><a href="#">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">Welcome to HubArchiveCreator’s documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+</ul>
+
+  <h4>Next topic</h4>
+  <p class="topless"><a href="code.html"
+                        title="next chapter">Auto Generated Documentation</a></p>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="_sources/index.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="code.html" title="Auto Generated Documentation"
+             >next</a> |</li>
+        <li class="nav-item nav-item-0"><a href="#">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        © Copyright 2016, Remi Marenco.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
+    </div>
+  </body>
+</html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/objects.inv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/objects.inv Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,7 @@
+# Sphinx inventory version 2
+# Project: HubArchiveCreator
+# Version: 2.3
+# The remainder of this file is compressed using zlib.
+xڥ�OK�0��#
+��uo��zC��m#I��b��ź��)ɛy�� r� j0;��ā�i�Xg�"��!9{^��f8��s��Bc7s�٫d��ODL!�J�G3��CɇZ&��+T�GҢ�&�w/��cN��|��|k͊�E�691��#� 5ݲ��W0Mo��ۧ��v6��
+x��w�W¢�V��Q.#�e�YS~�/��X�cM��Q��\�O�G�ʖ �
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/py-modindex.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/py-modindex.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,112 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+    <title>Python Module Index — HubArchiveCreator 2.3 documentation</title>
+
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '2.3',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" />
+
+
+    <script type="text/javascript">
+      DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
+    </script>
+
+
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="#" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+
+   <h1>Python Module Index</h1>
+
+   <div class="modindex-jumpbox">
+   <a href="#cap-h"><strong>h</strong></a>
+   </div>
+
+   <table class="indextable modindextable" cellspacing="0" cellpadding="2">
+     <tr class="pcap"><td></td><td> </td><td></td></tr>
+     <tr class="cap" id="cap-h"><td></td><td>
+       <strong>h</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="code.html#module-hubArchiveCreator"><code class="xref">hubArchiveCreator</code></a></td><td>
+       <em></em></td></tr>
+   </table>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="#" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        © Copyright 2016, Remi Marenco.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
+    </div>
+  </body>
+</html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/search.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/search.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,108 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+    <title>Search — HubArchiveCreator 2.3 documentation</title>
+
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '2.3',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script type="text/javascript" src="_static/searchtools.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="#" />
+    <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" />
+  <script type="text/javascript">
+    jQuery(function() { Search.loadIndex("searchindex.js"); });
+  </script>
+
+  <script type="text/javascript" id="searchindexloader"></script>
+
+
+  </head>
+  <body role="document">
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <h1 id="search-documentation">Search</h1>
+  <div id="fallback" class="admonition warning">
+  <script type="text/javascript">$('#fallback').hide();</script>
+  <p>
+    Please activate JavaScript to enable the search
+    functionality.
+  </p>
+  </div>
+  <p>
+    From here you can search these documents. Enter your search
+    words into the box below and click "search". Note that the search
+    function will automatically search for all of the words. Pages
+    containing fewer words won't appear in the result list.
+  </p>
+  <form action="" method="get">
+    <input type="text" name="q" value="" />
+    <input type="submit" value="search" />
+    <span id="search-progress" style="padding-left: 10px"></span>
+  </form>
+
+  <div id="search-results">
+
+  </div>
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li>
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        © Copyright 2016, Remi Marenco.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
+    </div>
+  </body>
+</html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/_build/html/searchindex.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/searchindex.js Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,1 @@
+Search.setIndex({envversion:49,filenames:["code","index"],objects:{"":{hubArchiveCreator:[0,0,0,"-"]},hubArchiveCreator:{configure_logger_dev:[0,1,1,""],configure_logger_stderr:[0,1,1,""],configure_logger_user:[0,1,1,""],create_ordered_datatype_objects:[0,1,1,""],sanitize_name_input:[0,1,1,""],sanitize_name_inputs:[0,1,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"break":0,"function":0,"return":0,access:0,all:0,also:0,argument:0,array_input:0,assembl:0,augustusdbia3:0,becaus:0,brute:0,can:0,charact:0,configur:0,configure_logger_dev:0,configure_logger_stderr:0,configure_logger_us:0,contain:0,content:1,could:0,create_ordered_datatype_object:0,creation:0,critical:0,data:0,datatyp:0,dbia3:0,debug:0,defin:0,dev:0,dict:0,dictionari:0,error:0,even:0,exampl:0,execut:0,extensionclass:0,file:0,folder:0,follow:0,format:0,from:0,full:0,further:0,galaxi:0,gff3:0,have:0,html:0,hub:0,hubarchivecr:[],index:1,input:0,inputs_data:0,just:0,kei:0,list:0,log:0,log_stdout:0,logger:0,modul:1,name:0,necessari:0,need:0,none:0,output:0,page:1,param:[],paramet:0,pass:0,path:0,permit:0,prepar:0,program:0,readi:0,replac:0,rtype:[],sanit:0,sanitize_name_input:0,search:1,should:0,sometim:0,sourc:0,space:0,special:0,stderr:0,stdout:0,still:0,string:0,string_to_sanit:0,test:0,thi:0,this_is_an__exampl:0,tool:0,traceback:0,trackhub:0,type:0,updat:0,user:0,valu:0,visual:0,warn:0,well:0,what:0,which:0,without:0,your:0},titles:["Auto Generated Documentation","Welcome to HubArchiveCreator’s documentation!"],titleterms:{auto:0,document:[0,1],gener:0,hubarchivecr:1,indice:1,tabl:1,welcom:1}})
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 doc/code.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/code.rst Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+Auto Generated Documentation
+============================
+
+.. automodule:: hubArchiveCreator
+ :members:

diff -r 000000000000 -r f493979f1408 doc/conf.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/conf.py Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,296 @@\n+# -*- coding: utf-8 -*-\n+#\n+# HubArchiveCreator documentation build configuration file, created by\n+# sphinx-quickstart on Thu Nov 3 11:43:14 2016.\n+#\n+# This file is execfile()d with the current directory set to its\n+# containing dir.\n+#\n+# Note that not all possible configuration values are present in this\n+# autogenerated file.\n+#\n+# All configuration values have a default; values that are commented out\n+# serve to show the default.\n+\n+import sys\n+import os\n+\n+# If extensions (or modules to document with autodoc) are in another directory,\n+# add these directories to sys.path here. If the directory is relative to the\n+# documentation root, use os.path.abspath to make it absolute, like shown here.\n+sys.path.insert(0, os.path.abspath(\'..\'))\n+\n+# -- General configuration ------------------------------------------------\n+\n+# If your documentation needs a minimal Sphinx version, state it here.\n+#needs_sphinx = \'1.0\'\n+\n+# Add any Sphinx extension module names here, as strings. They can be\n+# extensions coming with Sphinx (named \'sphinx.ext.*\') or your custom\n+# ones.\n+extensions = [\n+ \'sphinx.ext.autodoc\',\n+ \'sphinx.ext.doctest\',\n+ \'sphinx.ext.intersphinx\',\n+ \'sphinx.ext.todo\',\n+ \'sphinx.ext.coverage\',\n+ \'sphinx.ext.mathjax\',\n+ \'sphinx.ext.ifconfig\',\n+ \'sphinx.ext.viewcode\',\n+]\n+\n+# Add any paths that contain templates here, relative to this directory.\n+templates_path = [\'_templates\']\n+\n+# The suffix(es) of source filenames.\n+# You can specify multiple suffix as a list of string:\n+# source_suffix = [\'.rst\', \'.md\']\n+source_suffix = \'.rst\'\n+\n+# The encoding of source files.\n+#source_encoding = \'utf-8-sig\'\n+\n+# The master toctree document.\n+master_doc = \'index\'\n+\n+# General information about the project.\n+project = u\'HubArchiveCreator\'\n+copyright = u\'2016, Remi Marenco\'\n+author = u\'Remi Marenco\'\n+\n+# The version info for the project you\'re documenting, acts as replacement for\n+# |version| and |release|, also used in various other places throughout the\n+# built documents.\n+#\n+# The short X.Y version.\n+version = u\'2.3\'\n+# The full version, including alpha/beta/rc tags.\n+release = u\'2.3\'\n+\n+# The language for content autogenerated by Sphinx. Refer to documentation\n+# for a list of supported languages.\n+#\n+# This is also used if you do content translation via gettext catalogs.\n+# Usually you set "language" from the command line for these cases.\n+language = None\n+\n+# There are two options for replacing |today|: either, you set today to some\n+# non-false value, then it is used:\n+#today = \'\'\n+# Else, today_fmt is used as the format for a strftime call.\n+#today_fmt = \'%B %d, %Y\'\n+\n+# List of patterns, relative to source directory, that match files and\n+# directories to ignore when looking for source files.\n+exclude_patterns = [\'_build\']\n+\n+# The reST default role (used for this markup: `text`) to use for all\n+# documents.\n+#default_role = None\n+\n+# If true, \'()\' will be appended to :func: etc. cross-reference text.\n+#add_function_parentheses = True\n+\n+# If true, the current module name will be prepended to all description\n+# unit titles (such as .. function::).\n+#add_module_names = True\n+\n+# If true, sectionauthor and moduleauthor directives will be shown in the\n+# output. They are ignored by default.\n+#show_authors = False\n+\n+# The name of the Pygments (syntax highlighting) style to use.\n+pygments_style = \'sphinx\'\n+\n+# A list of ignored prefixes for module index sorting.\n+#modindex_common_prefix = []\n+\n+# If true, keep warnings as "system message" paragraphs in the built documents.\n+#keep_warnings = False\n+\n+# If true, `todo` and `todoList` produce output, else they produce nothing.\n+todo_include_todos = True\n+\n+\n+# -- Options for HTML output ----------------------------------------------\n+\n+# The theme to use for HTML and HTML Help pages. See the documentation for\n+# a list of builtin themes.\n+html_theme = \'classic\'\n+\n+# Theme options are theme-specific and customize the look and feel of a them'..b'ex is split into individual pages for each letter.\n+#html_split_index = False\n+\n+# If true, links to the reST sources are added to the pages.\n+#html_show_sourcelink = True\n+\n+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.\n+#html_show_sphinx = True\n+\n+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.\n+#html_show_copyright = True\n+\n+# If true, an OpenSearch description file will be output, and all pages will\n+# contain a <link> tag referring to it. The value of this option must be the\n+# base URL from which the finished HTML is served.\n+#html_use_opensearch = \'\'\n+\n+# This is the file name suffix for HTML files (e.g. ".xhtml").\n+#html_file_suffix = None\n+\n+# Language to be used for generating the HTML full-text search index.\n+# Sphinx supports the following languages:\n+# \'da\', \'de\', \'en\', \'es\', \'fi\', \'fr\', \'hu\', \'it\', \'ja\'\n+# \'nl\', \'no\', \'pt\', \'ro\', \'ru\', \'sv\', \'tr\'\n+#html_search_language = \'en\'\n+\n+# A dictionary with options for the search language support, empty by default.\n+# Now only \'ja\' uses this config value\n+#html_search_options = {\'type\': \'default\'}\n+\n+# The name of a javascript file (relative to the configuration directory) that\n+# implements a search results scorer. If empty, the default will be used.\n+#html_search_scorer = \'scorer.js\'\n+\n+# Output file base name for HTML help builder.\n+htmlhelp_basename = \'HubArchiveCreatordoc\'\n+\n+# -- Options for LaTeX output ---------------------------------------------\n+\n+latex_elements = {\n+# The paper size (\'letterpaper\' or \'a4paper\').\n+#\'papersize\': \'letterpaper\',\n+\n+# The font size (\'10pt\', \'11pt\' or \'12pt\').\n+#\'pointsize\': \'10pt\',\n+\n+# Additional stuff for the LaTeX preamble.\n+#\'preamble\': \'\',\n+\n+# Latex figure (float) alignment\n+#\'figure_align\': \'htbp\',\n+}\n+\n+# Grouping the document tree into LaTeX files. List of tuples\n+# (source start file, target name, title,\n+# author, documentclass [howto, manual, or own class]).\n+latex_documents = [\n+ (master_doc, \'HubArchiveCreator.tex\', u\'HubArchiveCreator Documentation\',\n+ u\'Remi Marenco\', \'manual\'),\n+]\n+\n+# The name of an image file (relative to this directory) to place at the top of\n+# the title page.\n+#latex_logo = None\n+\n+# For "manual" documents, if this is true, then toplevel headings are parts,\n+# not chapters.\n+#latex_use_parts = False\n+\n+# If true, show page references after internal links.\n+#latex_show_pagerefs = False\n+\n+# If true, show URL addresses after external links.\n+#latex_show_urls = False\n+\n+# Documents to append as an appendix to all manuals.\n+#latex_appendices = []\n+\n+# If false, no module index is generated.\n+#latex_domain_indices = True\n+\n+\n+# -- Options for manual page output ---------------------------------------\n+\n+# One entry per manual page. List of tuples\n+# (source start file, name, description, authors, manual section).\n+man_pages = [\n+ (master_doc, \'hubarchivecreator\', u\'HubArchiveCreator Documentation\',\n+ [author], 1)\n+]\n+\n+# If true, show URL addresses after external links.\n+#man_show_urls = False\n+\n+\n+# -- Options for Texinfo output -------------------------------------------\n+\n+# Grouping the document tree into Texinfo files. List of tuples\n+# (source start file, target name, title, author,\n+# dir menu entry, description, category)\n+texinfo_documents = [\n+ (master_doc, \'HubArchiveCreator\', u\'HubArchiveCreator Documentation\',\n+ author, \'HubArchiveCreator\', \'One line description of project.\',\n+ \'Miscellaneous\'),\n+]\n+\n+# Documents to append as an appendix to all manuals.\n+#texinfo_appendices = []\n+\n+# If false, no module index is generated.\n+#texinfo_domain_indices = True\n+\n+# How to display URL addresses: \'footnote\', \'no\', or \'inline\'.\n+#texinfo_show_urls = \'footnote\'\n+\n+# If true, do not generate a @detailmenu in the "Top" node\'s menu.\n+#texinfo_no_detailmenu = False\n+\n+\n+# Example configuration for intersphinx: refer to the Python standard library.\n+intersphinx_mapping = {\'https://docs.python.org/\': None}\n'

diff -r 000000000000 -r f493979f1408 doc/index.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/index.rst Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 doc/make.bat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/make.bat Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,263 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+ set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+ set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+ :help
+ echo.Please use `make ^<target^>` where ^<target^> is one of
+ echo.  html       to make standalone HTML files
+ echo.  dirhtml    to make HTML files named index.html in directories
+ echo.  singlehtml to make a single large HTML file
+ echo.  pickle     to make pickle files
+ echo.  json       to make JSON files
+ echo.  htmlhelp   to make HTML files and a HTML help project
+ echo.  qthelp     to make HTML files and a qthelp project
+ echo.  devhelp    to make HTML files and a Devhelp project
+ echo.  epub       to make an epub
+ echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo.  text       to make text files
+ echo.  man        to make manual pages
+ echo.  texinfo    to make Texinfo files
+ echo.  gettext    to make PO message catalogs
+ echo.  changes    to make an overview over all changed/added/deprecated items
+ echo.  xml        to make Docutils-native XML files
+ echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+ echo.  linkcheck  to check all external links for integrity
+ echo.  doctest    to run all doctests embedded in the documentation if enabled
+ echo.  coverage   to run coverage check of the documentation if enabled
+ goto end
+)
+
+if "%1" == "clean" (
+ for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+ del /q /s %BUILDDIR%\*
+ goto end
+)
+
+
+REM Check if sphinx-build is available and fallback to Python version if any
+%SPHINXBUILD% 1>NUL 2>NUL
+if errorlevel 9009 goto sphinx_python
+goto sphinx_ok
+
+:sphinx_python
+
+set SPHINXBUILD=python -m sphinx.__init__
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+:sphinx_ok
+
+
+if "%1" == "html" (
+ %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+ goto end
+)
+
+if "%1" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+ goto end
+)
+
+if "%1" == "singlehtml" (
+ %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+ echo.^> qcollectiongenerator %BUILDDIR%\qthelp\HubArchiveCreator.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile %BUILDDIR%\qthelp\HubArchiveCreator.ghc
+ goto end
+)
+
+if "%1" == "devhelp" (
+ %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished.
+ goto end
+)
+
+if "%1" == "epub" (
+ %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The epub file is in %BUILDDIR%/epub.
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdf" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf
+ cd %~dp0
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "latexpdfja" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+ cd %BUILDDIR%/latex
+ make all-pdf-ja
+ cd %~dp0
+ echo.
+ echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+ goto end
+)
+
+if "%1" == "text" (
+ %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The text files are in %BUILDDIR%/text.
+ goto end
+)
+
+if "%1" == "man" (
+ %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The manual pages are in %BUILDDIR%/man.
+ goto end
+)
+
+if "%1" == "texinfo" (
+ %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+ goto end
+)
+
+if "%1" == "gettext" (
+ %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.The overview file is in %BUILDDIR%/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+ goto end
+)
+
+if "%1" == "doctest" (
+ %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+ goto end
+)
+
+if "%1" == "coverage" (
+ %SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Testing of coverage in the sources finished, look at the ^
+results in %BUILDDIR%/coverage/python.txt.
+ goto end
+)
+
+if "%1" == "xml" (
+ %SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The XML files are in %BUILDDIR%/xml.
+ goto end
+)
+
+if "%1" == "pseudoxml" (
+ %SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+ if errorlevel 1 exit /b 1
+ echo.
+ echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+ goto end
+)
+
+:end

diff -r 000000000000 -r f493979f1408 hubArchiveCreator.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hubArchiveCreator.py Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,315 @@\n+#!/usr/bin/python\n+# -*- coding: utf8 -*-\n+\n+"""\n+This Galaxy tool permits to prepare your files to be ready for\n+Assembly Hub visualization.\n+Program test arguments:\n+hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html\n+"""\n+\n+import argparse\n+import collections\n+import json\n+import logging\n+import os\n+import sys\n+\n+# Internal dependencies\n+from Bam import Bam\n+from BedSimpleRepeats import BedSimpleRepeats\n+from BedSpliceJunctions import BedSpliceJunctions\n+from Bed import Bed\n+from BigWig import BigWig\n+from util.Fasta import Fasta\n+from util.Filters import TraceBackFormatter\n+from Gff3 import Gff3\n+from Gtf import Gtf\n+from Psl import Psl\n+from TrackHub import TrackHub\n+\n+# TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort\n+\n+\n+def main(argv):\n+ # Command Line parsing init\n+ parser = argparse.ArgumentParser(description=\'Create a foo.txt inside the given folder.\')\n+\n+ # Reference genome mandatory\n+ parser.add_argument(\'-f\', \'--fasta\', help=\'Fasta file of the reference genome\')\n+\n+ # GFF3 Management\n+ parser.add_argument(\'--gff3\', action=\'append\', help=\'GFF3 format\')\n+\n+ # GTF Management\n+ parser.add_argument(\'--gtf\', action=\'append\', help=\'GTF format\')\n+\n+ # Bed4+12 (TrfBig)\n+ parser.add_argument(\'--bedSimpleRepeats\', action=\'append\', help=\'Bed4+12 format, using simpleRepeats.as\')\n+\n+ # Bed12+1 (regtools)\n+ parser.add_argument(\'--bedSpliceJunctions\', action=\'append\', help=\'Bed12+1 format, using spliceJunctions.as\')\n+\n+ # Generic Bed (Blastx transformed to bed)\n+ parser.add_argument(\'--bed\', action=\'append\', help=\'Bed generic format\')\n+\n+ # BigWig Management\n+ parser.add_argument(\'--bigwig\', action=\'append\', help=\'BigWig format\')\n+\n+ # Bam Management\n+ parser.add_argument(\'--bam\', action=\'append\', help=\'Bam format\')\n+\n+ # Psl Management\n+ parser.add_argument(\'--psl\', action=\'append\', help=\'Psl format\')\n+\n+ # TODO: Check if the running directory can have issues if we run the tool outside\n+ parser.add_argument(\'-d\', \'--directory\',\n+ help=\'Running tool directory, where to find the templates. Default is running directory\')\n+ parser.add_argument(\'-u\', \'--ucsc_tools_path\',\n+ help=\'Directory where to find the executables needed to run this tool\')\n+ parser.add_argument(\'-e\', \'--extra_files_path\',\n+ help=\'Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive\')\n+ parser.add_argument(\'-o\', \'--output\', help=\'Name of the HTML summarizing the content of the Track Hub Archive\')\n+\n+ parser.add_argument(\'-j\', \'--data_json\', help=\'Json containing the metadata of the inputs\')\n+\n+ parser.add_argument(\'--user_email\', help=\'Email of the user who launched the Hub Archive Creation\')\n+\n+ parser.add_argument(\'--genome_name\', help=\'UCSC Genome Browser assembly ID\')\n+\n+ parser.add_argument(\'--debug_mode\', action=\'store_true\', help=\'Allow more details about the errors\')\n+\n+ # Begin init variables\n+\n+ toolDirectory = \'.\'\n+ extra_files_path = \'.\'\n+\n+ # Get the args passed in parameter\n+ args = parser.parse_args()\n+\n+ extra_files_path = args.extra_files_path\n+ toolDirectory = args.directory\n+\n+ #### Logging management ####\n+ # If we are in Debug mode, also print in stdout the debug dump\n+\n+ configure_logger(extra_files_path=extra_files_path, debug=args.debug_mode)\n+\n+ #### END Logging management ####\n+\n+ array_inputs_reference_genome = json.loads(args.fasta)\n+\n+ # TODO: Replace these with the object Fasta\n+ input_fasta_file = array_inputs_reference_genome["false_path"]\n+ input_fasta_file_name = sanitize_name_input(array_inputs_reference_genome["name"])\n+ genome_name = sanitize_name_input(args.genome_name)\n+\n+ reference_genome = Fasta(input_fasta_file,\n+ '..b'output from Galaxy, or even just file name, from user inputs, have spaces.\n+ Also, it can contain \'/\' character and could break the use of os.path function.\n+\n+ :param inputs_data: dict[string, dict[string, string]]\n+ """\n+ for key in inputs_data:\n+ inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])\n+\n+\n+def create_ordered_datatype_objects(ExtensionClass, array_inputs, inputs_data):\n+ """\n+ Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub\n+ and update the dictionary of datatype\n+\n+ :param ExtensionClass:\n+ :param array_inputs:\n+ :param inputs_data:\n+ :type ExtensionClass: Datatype\n+ :type array_inputs: list[string]\n+ :type inputs_data: dict\n+ :rtype: dict\n+ """\n+\n+ datatype_dictionary = {}\n+\n+ # TODO: Optimize this double loop\n+ for input_false_path in array_inputs:\n+ for key, data_value in inputs_data.items():\n+ if key == input_false_path:\n+ logging.debug("input_false_path: " + input_false_path)\n+ logging.debug("data_value: " + str(data_value))\n+ extensionObject = ExtensionClass(input_false_path, data_value)\n+ datatype_dictionary.update({data_value["order_index"]: extensionObject})\n+ return datatype_dictionary\n+\n+def configure_logger(extra_files_path=None, debug=False):\n+ if not extra_files_path:\n+ raise Exception("Extra files path is not set. Stopping the application")\n+\n+\n+ # All case log: log everything in a .log file\n+ logger_file_name = \'\'.join([__name__, \'.log\'])\n+ logging_file_path = os.path.join(extra_files_path, logger_file_name)\n+\n+ logging.basicConfig(filename=logging_file_path, level=logging.DEBUG)\n+\n+ log_stdout = logging.StreamHandler(sys.stdout)\n+ if not debug:\n+ configure_logger_user(log_stdout)\n+ else:\n+ configure_logger_dev(log_stdout)\n+\n+ # stderr configuration\n+ configure_logger_stderr()\n+\n+ logging.debug(\'#### Welcome in HubArchiveCreator Debug Mode ####\\n\')\n+\n+def configure_logger_user(log_stdout=None):\n+ """\n+ User Logger is defined as following:\n+ - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback\n+ in STDOUT\n+ - Still access to full, brute and traceback for errors\n+ in STDERR\n+ - And further access to debug if needed\n+ in .log\n+\n+ """\n+\n+ if not log_stdout:\n+ raise Exception("No log_stdout given. Stopping the application")\n+\n+ # stdout for INFO / WARN / ERROR / CRITICAL\n+ log_stdout.setLevel(logging.INFO)\n+\n+ formatter = TraceBackFormatter(\'%(message)s\')\n+\n+ log_stdout.setFormatter(formatter)\n+\n+ logging.getLogger().addHandler(log_stdout)\n+\n+def configure_logger_dev(log_stdout=None):\n+ """\n+ Dev Logger is defined as following:\n+ - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout\n+ - Still access to full, brute and traceback in stderr for errors\n+ - And further access to debug if needed\n+\n+ """\n+ if not log_stdout:\n+ raise Exception("No log_stdout given. Stopping the application")\n+ log_format = \'%(message)s\'\n+\n+ # stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL\n+ log_stdout.setLevel(logging.DEBUG)\n+\n+ formatter = logging.Formatter(log_format)\n+\n+ log_stdout.setFormatter(formatter)\n+\n+ logging.getLogger().addHandler(log_stdout)\n+\n+def configure_logger_stderr():\n+ """\n+ Configure what should be logged in stderr\n+ """\n+ log_error = logging.StreamHandler(sys.stderr)\n+ log_error.setLevel(logging.ERROR)\n+ log_error_format = \'%(message)s\'\n+\n+ formatter_error = logging.Formatter(log_error_format)\n+\n+ log_error.setFormatter(formatter_error)\n+\n+ logging.getLogger().addHandler(log_error)\n+\n+if __name__ == "__main__":\n+ logging.getLogger(__name__)\n+ main(sys.argv)\n'

diff -r 000000000000 -r f493979f1408 hubArchiveCreator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hubArchiveCreator.xml Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,1014 @@\n+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">\n+ <description>\n+ This Galaxy tool permits to prepare your files to be ready for\n+ Assembly Hub visualization.\n+ </description>\n+\n+ <requirements>\n+ \n+ <requirement type="package" version="332">ucsc-bedtobigbed</requirement>\n+ <requirement type="package" version="332">ucsc-fatotwobit</requirement>\n+ <requirement type="package" version="332">ucsc-genepredtobed</requirement>\n+ <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>\n+ <requirement type="package" version="332">ucsc-gff3togenepred</requirement>\n+ <requirement type="package" version="332">ucsc-gtftogenepred</requirement>\n+ \n+ \n+ <requirement type="package" version="332">ucsc-twobitinfo</requirement>\n+ <requirement type="package" version="1.3">samtools</requirement>\n+ \n+ <requirement type="package" version="312">ucsc_tools</requirement>\n+ <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>\n+ <requirement type="package" version="0.0.1">gtfToGenePred</requirement>\n+ <requirement type="package" version="0.0.1">genePredToBed</requirement>\n+ <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>\n+ <requirement type="package" version="0.0.1">pslToBigPsl</requirement>\n+ <requirement type="package" version="1.2">samtools</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <regex match="^pass1"\n+ source="stderr"\n+ level="log"\n+ description="bedToBigBed"/>\n+ \n+ \n+ </stdio>\n+\n+ \n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir -p $output.extra_files_path;\n+\n+ python $__tool_directory__/hubArchiveCreator.py\n+\n+ ## Ask the user to enter the genome name\n+ --genome_name \'$genome_name\'\n+\n+ #import json\n+\n+ #set global data_parameter_dict = {}\n+\n+ ## Function to retrieve the data of the inputs\n+ #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={})\n+ #set false_path = str($input_to_prepare)\n+ #set name = $input_to_prepare.name\n+\n+ #set data_dict = {"name": $name}\n+ #silent data_dict.update($extra_data_dict)\n+\n+ ## Add the ordering by taking the tool form indexes\n+ #silent $data_dict.update({"order_index": $order_index})\n+\n+ #silent $data_parameter_dict.update({$false_path: $data_dict})\n+\n+ #end def\n+\n+\n+ ## Get the number of digits from tracks, to have a unique integer from group index and track index\n+\n+ #set temp_max_digit = 0\n+\n+ #for $g in $group\n+ #if len($g.format) > $temp_max_digit\n+ #silent temp_max_digit = len($g.format)\n+ #end if\n+ #end for\n+\n+ #set nb_digits_max_track = len(str($temp_max_digit))\n+\n+ ## END Get the number of digits\n+\n+ #for $i_g, $g in enumerate( $group )\n+ #for $i, $f in enumerate( $g.format )\n+ ## Create the order index using index_group+1 concatenated with index_track\n+ #set index_group_final = str($i_g + 1)\n+ #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)\n+\n+ ## For each format, we have a few mandatory fields we store in a dict\n+ #set track_color = str($f.formatChoice.track_color)\n+ #set'..b'lt group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="bam"/>\n+ <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>\n+ <param name="track_color" value="#000000"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="default_color/default_color_trackhub.html">\n+ \n+ <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt">\n+ <assert_contents>\n+ <has_text text="color 0,0,0"/>\n+ </assert_contents>\n+ </extra_files>\n+\n+ \n+ </output>\n+ </test>\n+\n+ \n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ <param name="fasta_file" value="common/dbia3.fa"/>\n+ <repeat name="group">\n+ <param name="group_name" value="Default group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="bam"/>\n+ <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>\n+ <param name="track_color" value="#8064a2"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="changed_color/changed_color_trackhub.html">\n+ \n+ <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt">\n+ <assert_contents>\n+ <has_text text="color 128,100,162"/>\n+ </assert_contents>\n+ </extra_files>\n+\n+ \n+ </output>\n+ </test>\n+\n+ \n+ <test>\n+ <param name="genome_name" value="Dbia3"/>\n+ <param name="fasta_file" value="common/dbia3.fa"/>\n+ <repeat name="group">\n+ <param name="group_name" value="Default group"/>\n+ <repeat name="format">\n+ <conditional name="formatChoice">\n+ <param name="format_select" value="gtf"/>\n+ <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/>\n+ <param name="track_color" value="#000000"/>\n+ </conditional>\n+ </repeat>\n+ </repeat>\n+ <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html">\n+ <extra_files type="file"\n+ name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"\n+ value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"\n+ compare="sim_size"\n+ />\n+\n+ \n+ </output>\n+ </test>\n+\n+ \n+\n+ \n+\n+ </tests>\n+\n+ <help>\n+ This Galaxy tool permits to prepare your files to be ready for\n+ Assembly Hub visualization.\n+ </help>\n+</tool>\n'

diff -r 000000000000 -r f493979f1408 spliceJunctions.as
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/spliceJunctions.as Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,17 @@
+table spliceJunctions
+"Predicted splice junctions"
+    (
+    string chrom;      "Reference sequence chromosome or scaffold"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Name of item"
+    uint   score;      "Score from 0-1000"
+    char[1] strand;    "+ or -"
+    uint thickStart;   "Start of where display should be thick (start codon)"
+    uint thickEnd;     "End of where display should be thick (stop codon)"
+    uint reserved;     "Used as itemRgb as of 2004-11-22"
+    int blockCount;    "Number of blocks"
+    int[blockCount] blockSizes; "Comma separated list of block sizes"
+    int[blockCount] chromStarts; "Start positions relative to chromStart"
+    uint junctionScore;   "Number of reads supporting the splice junction"
+    )

diff -r 000000000000 -r f493979f1408 templates/display.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/display.txt Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,52 @@
+<%namespace name="os" module="os"/>
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+            ${print_tree(walkable_tree)}
+        </ul>
+    </body>
+</html>
+
+<%def name="print_tree(tree)">
+    % if len(tree) == 0:
+        ## We do nothing, we are called by a leaf
+        ## If we are there, this is not normal though
+        ## TODO: Manage the error
+        return
+    % else:
+        % for vertex in tree:
+            % if len(tree[vertex][0]) > 0:
+                <li>
+                    ${vertex}
+                </li>
+                <ul>
+                    ${print_tree(tree[vertex][0])}
+                </ul>
+            % else:
+                <li>
+                    <a href="${tree[vertex][1]}">${vertex}</a>
+                </li>
+            % endif
+        % endfor
+    % endif
+</%def>
+
+<%doc>
+    def recurse_print_tree(tree, level):
+        if len(tree) == 0:
+            return
+
+        for vertex in tree:
+            composite_name = vertex
+            bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name)
+            rval.append(bullet_point)
+            # Parent, so need to create a sub <ul>
+            if len(tree[vertex]) > 0:
+                rval.append('<ul>')
+                print_tree(tree[vertex], level+1)
+                rval.append('</ul>')
+
+</%doc>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 templates/genomesAssembly/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/genomesAssembly/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+## TODO: Add a loop to be able to put this template for each genome
+genome ${genomeName}
+trackDb ${trackDbPath}
+groups ${groupsPath}
+description ${genomeDescription}
+twoBitPath ${twoBitPath}
+organism ${organismName}
+defaultPos ${defaultPosition}
+orderKey ${orderKey}
+scientificName ${scientificName}
+htmlPath ${pathAssemblyHtmlDescription}

diff -r 000000000000 -r f493979f1408 templates/groupsTxt/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/groupsTxt/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name ${label.lower().replace(' ', '_')}
+label ${label}
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 templates/hubDescription/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/hubDescription/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+<html>
+<body>
+ ${specie} genome with ${toolUsed}
+ <a href="${ncbiSpecieUrl}">NCBI genome/${genomeID} (${specieFullName})</a>
+</body>
+</html>

diff -r 000000000000 -r f493979f1408 templates/hubTxt/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/hubTxt/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub ${hubName}
+shortLabel ${shortLabel}
+longLabel ${longLabel}
+genomesFile ${genomesFile}
+email ${email}
+descriptionUrl ${descriptionUrl}

diff -r 000000000000 -r f493979f1408 templates/specieDescription/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/specieDescription/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+<html>
+<body>
+ ${specieDescription}
+</body>
+</html>

diff -r 000000000000 -r f493979f1408 templates/trackDb/layout.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/trackDb/layout.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,14 @@
+% for trackDb in trackDbs:
+    ## See this http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
+    track ${trackDb.trackName}
+    longLabel ${trackDb.longLabel}
+    shortLabel ${trackDb.shortLabel}
+    bigDataUrl ${trackDb.trackDataURL}
+    type ${trackDb.trackType}
+    visibility ${trackDb.visibility}
+    thickDrawItem ${trackDb.thickDrawItem}
+    priority ${trackDb.priority}
+    color ${trackDb.track_color}
+    group ${trackDb.group_name.lower().replace(' ', '_')}
+
+% endfor

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,120 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2738.dat
+DEBUG:root:data_value: {u'index': u'/home/galaxy/Dev/galaxy/database/files/_metadata_files/000/metadata_61.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits.bam', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2739.dat
+DEBUG:root:data_value: {u'order_index': u'11', u'name': u'TBLASTN_Alignment_to_proteins', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpgvTufo.sortedBed
+DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb
+DEBUG:root:typeOption: None
+DEBUG:root:autoSql: None
+DEBUG:root:tab option: False
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2742.dat
+DEBUG:root:data_value: {u'order_index': u'14', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2740.dat
+DEBUG:root:data_value: {u'order_index': u'12', u'name': u'Repeating_Elements_by_TrfBig', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpn63XX6.sortedBed
+DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb
+DEBUG:root:typeOption: bed4+12
+DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/trf_simpleRepeat.as
+DEBUG:root:tab option: False
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2743.dat
+DEBUG:root:data_value: {u'order_index': u'15', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gff3ToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp6noWC0.sorted.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2744.dat
+DEBUG:root:data_value: {u'order_index': u'16', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp9EgTcK.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/galaxy/Dev/galaxy/database/files/002/dataset_2741.dat
+DEBUG:root:data_value: {u'order_index': u'13', u'name': u'blastXmlToPsl', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling pslToBigPsl:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Hello
+DEBUG:root:sorted_bed_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmpB6cFUgpsl
+DEBUG:root:chrom_sizes_file_name: /home/galaxy/Dev/galaxy/database/tmp/tmp1Hz50C.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/tracks/blastXmlToPsl.bb
+DEBUG:root:typeOption: bed12+12
+DEBUG:root:autoSql: /home/galaxy/Dev/galaxy/tools/hub-archive-creator/bigPsl.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bed.Bed object at 0x7f91d06b5fd0>, <Bam.Bam object at 0x7f91d06b5e50>, <Psl.Psl object at 0x7f91d06b5910>, <BedSimpleRepeats.BedSimpleRepeats object at 0x7f91d06b5b10>, <Gff3.Gff3 object at 0x7f91d06b5c90>, <BigWig.BigWig object at 0x7f91d06b5990>, <Gtf.Gtf object at 0x7f91d06b57d0>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track TBLASTN_Alignment_to_proteins.bb (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track blastXmlToPsl.bb (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Repeating_Elements_by_TrfBig.bb (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
+DEBUG:root:We DON'T add in /home/galaxy/Dev/galaxy/database/jobs_directory/001/1302/dataset_2746_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/all_datatypes_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/all_datatypes_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,91 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/Dbia3.2bit

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,77 @@
+    track TBLASTN_Alignment_to_proteins.bb
+    longLabel TBLASTN Alignment to proteins
+    shortLabel TBLASTN Alignme
+    bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb
+    type bigBed
+    visibility dense
+    thickDrawItem off
+    priority 11
+    color 0,0,0
+    group default_group
+
+    track HISAT2_Accepted_Hits.bam
+    longLabel HISAT2 Accepted Hits.bam
+    shortLabel HISAT2 Accepted
+    bigDataUrl tracks/HISAT2_Accepted_Hits.bam
+    type bam
+    visibility pack
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+
+    track blastXmlToPsl.bb
+    longLabel blastXmlToPsl
+    shortLabel blastXmlToPsl
+    bigDataUrl tracks/blastXmlToPsl.bb
+    type bigPsl
+    visibility dense
+    thickDrawItem off
+    priority 13
+    color 0,0,0
+    group default_group
+
+    track Repeating_Elements_by_TrfBig.bb
+    longLabel Repeating Elements by TrfBig
+    shortLabel Repeating Eleme
+    bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb
+    type bigBed 4 +
+    visibility dense
+    thickDrawItem off
+    priority 12
+    color 0,0,0
+    group default_group
+
+    track Augustus_Gene_Predictions.bb
+    longLabel Augustus Gene Predictions
+    shortLabel Augustus Gene P
+    bigDataUrl tracks/Augustus_Gene_Predictions.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 15
+    color 0,0,0
+    group default_group
+
+    track RNA-Seq_Alignment_Summary.bigwig
+    longLabel RNA-Seq Alignment Summary
+    shortLabel RNA-Seq Alignme
+    bigDataUrl tracks/RNA-Seq_Alignment_Summary.bigwig
+    type bigWig
+    visibility full
+    thickDrawItem off
+    priority 14
+    color 0,0,0
+    group default_group
+
+    track StringTie_Assembled_Transcripts.bb
+    longLabel StringTie Assembled Transcripts
+    shortLabel StringTie Assem
+    bigDataUrl tracks/StringTie_Assembled_Transcripts.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 16
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb

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diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+genome Dbia3
+trackDb Dbia3/trackDb.txt
+groups Dbia3/groups.txt
+description Dbia3
+twoBitPath Dbia3/Dbia3.2bit
+organism Dbia3
+defaultPos contig25
+orderKey 4500
+scientificName Dbia3
+htmlPath Dbia3/description.html

diff -r 000000000000 -r f493979f1408 test-data/all_datatypes/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_datatypes/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/augustus/hubaInputs/GTF/augustusDbia3.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustus/hubaInputs/GTF/augustusDbia3.gtf Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,7076 @@\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/galaxy/galaxy/dependency_dir/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# fly version. Using default transition matrix.\n+# Looks like /home/galaxy/galaxy/database/files/000/dataset_2.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Constraints/Hints:\n+# (none)\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+contig1\tAUGUSTUS\tgene\t553\t34688\t0.03\t-\t.\tcontig1.g1\n+contig1\tAUGUSTUS\ttranscript\t553\t34688\t0.03\t-\t.\tcontig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t553\t578\t0.41\t-\t2\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t652\t1047\t0.25\t-\t2\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t12541\t12968\t0.87\t-\t1\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t32202\t33826\t0.89\t-\t0\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t33880\t34044\t0.98\t-\t0\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t34107\t34619\t0.99\t-\t0\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tCDS\t34674\t34688\t0.45\t-\t0\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+contig1\tAUGUSTUS\tstart_codon\t34686\t34688\t.\t-\t0\ttranscript_id "contig1.g1.t1"; gene_id "contig1.g1";\n+# coding sequence = [atggcagcactctcgcaaaaggactttaatgacggaaaccagagaaatcgtcagaggaaaagtactgtcactgagcagc\n+# cctcatcaacatcaggaagcgtggcccaagtagaagcggacagcgcatcgtcacatttgtctgatcgctgttataacaacatagcaagtactaccaaa\n+# agtattgttggtgatgtgaaaacaagcagacgctgtgaagactttataagtagtggatcagcttcgactccattaaatgaatatgattgtgccaacgc\n+# tgatacgacggatattaaagatgaacctggagattttatagaaacaaattgtcattggcgaagttgttgtattgaatttaatacgcaagatgagcttg\n+# ttaaacatatcaataatgaccatatccaaaccaataagaaggcctttgtctgtcgatgggaaaattgtacccgtggtgaaaaacctttcaaagcgcag\n+# tatatgctagttgtgcatatgcgtcgtcataccggcgaaaagccacataaatgcacatttgaaggctgttttaaggcatattcacgcttggaaaacct\n+# aaaaacacatttacggtcacacacaggtgaaaaaccctatatgtgcgagtatccgggatgcagcaaggcgtttagtaatgcaagcgatcgtgcaaagc\n+# atcaaaatcgtactcacagtaatgagaaaccgtacatttgtaaagctcctggttgcacgaaacgttacaccgacccaagttctttgcgtaaacatgtt\n+# aaaacagttcatggtgctgagttttatgctaataaaaaacacaagggattgcccctaaatgatgcgaactctcgcctccaccgagacagtggccaagg\n+# tcggcataatcttcaagagcataatattgactctagcccttgcagcgaagaacttcaggtgggaaaacttataggcatgtctagtcccagtattaaat\n+# ctgaatctgatgaaagttcaccacatcatcagttgttaagtggagttcgagcttcagactgttttttaacatattcacaagatggtgccgccgaacat\n+# ataactttagatgacggctgggattgtgacgatgacgttgacgtggccgacttaccaattgtcttgcgtgctatggtaaatgttggcagcggaaattc\n+# gatggccccgaccattggagggggtgttgttgcgaggcagcgatttagaagtcgtttgcaaactaaaggaataaactctagtatggttatgcttggca\n+# acatccccgaaagcaatcgcaccattggaataagcgaacttaaccagcgtataacagaacttaagatggagcctggtaccgcttgtgatattacagtt\n+# ccattgaatacggggctggaaaggatttcagaagacttatcacaaaatcaatcaaatataacattaaataagcaaagcttctttaccgcttccggctc\n+# tctccaaggacattttcgtcgcgatagccagaactccactgcaagtacatattatggtagcatgcaaagtcgccgcagtagtcaatcatctcaggtgt\n+# cttctatatctacaatgcgtccaggcccatcgtacaacacaaccacagcttccctctatgatccaatttccccaggatgctctcgacgctctagccaa\n+# atgtctaatgtagtcaactcctacgcacttacatcaacatcaggattgactgcaattaacaaggacttaaatgcaaacagcagcccaaatgcttctat\n+# taataaaccgggtcttggtggtcagtactttggtttttacaataacagtcttcctccacctccatcgtctcatttaattgccaccaatttgaagcatc\n+# tgcaggacacagactctaggagttgttatcacaacacaactggcggtcgattttccattcccaattgtacgccatctctacatttagactacaat'..b'agt\n+# tttcgtgttggacgaatattgcgctcgctatggtgtgcggggatgctaccgacatttatgctacctttctgatttactggatcgtgcagaaaagcaac\n+# acatgatagatccaacactaattcactattcatttgcgttttgcgcaagccacgttcacggaaatcgacctgatggggtaggaagcattacgcatgag\n+# gaaaaggaaaaattttctgaaatcaaagaacgcctacgtcagttactggagtttcaaataaccaattttagatactgttttcctttcggtcgccccga\n+# aggcgctcttaaagcgacattatctttactagagagagtgctaatgaaagacattgttacccctgttccacctgaagaagttcgtcaaatgattaaaa\n+# aaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcacttttccgttcaagggacacgtgccagggaaa\n+# tcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctatcggaaaggtcccagggaaatcccgtcgga\n+# tattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagcagaactttgtgttgatctgttgcaacaaa\n+# atgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatgatgatgtaccaaaaggccacaatgaaagc\n+# gatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaatggatcgtcatttcgttattataatttgag\n+# gaatgggcgttttcatcagcacctgcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcata\n+# agggatttgaaaaagaacgctgggaaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataaga\n+# gacctgcactggccagacgcagagtttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactga\n+# ttcgtcttttcagtcgtggctaaaaaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattag\n+# atgctaaaaatcaaagctttaaattgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgta\n+# gctatgacacaaggtctaactggtaaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgat\n+# tcttagttttacaaatgtatcgagctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattg\n+# gcgacgatttatggaccctgaatttctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctg\n+# cactacgctcaagtttcatctatttctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagc\n+# atatcaagcagtcgcacagcgaatggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgag\n+# aaggggaagaagaagatactggcgacgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttacc\n+# aacgttgttgccggccgtgtgggtaatttactcggcaaaggcattggcggccttagttcaaagttgggaagtggaagttggttttaa]\n+# protein sequence = [MIDPSSSEEEGEDDPIANVSSKGRLTHAPKGTNTVSILGGVSGPGVGSNMAISGSNGDLAGNQRQSNISSISNRNDAG\n+# NVAGVGGSSNKNEQIHGSRVDGGNLEVPNSCIPSGVSQETLNQSIGSSRANSLPRPLSPSPSLTSEKPDTGDPHAFLKGETQIMADEAFQNAVQSYHD\n+# VFLKSERVLKMVQSGASSQHDFREVFRNNIEKRVRSLPEIDGLSKETVLTSWMAKFDIILKGTGEEDSKRPSRMQQSLNSELILSKEQLYDMFQQILL\n+# VKKFEHQILYNALMLDSADEQAAAIRRELDGRMQRVGEMEKNRKLMPKFVLKEMESLYVEELKSSINLLMANLESLPVSKGNMDSKYGLQKLKRYNHR\n+# KLILRSHGSLSKLEGDSEDGSTQLTKLDVVLTFQLEVIVMEVKGLKSLAPNRIVYCTMEVENGEKLQTDQAEASKPMWDTQGDFTTTHPLPVVKVKLY\n+# TENPGMLALEDKELGKVILKPTPLSSKSPEWHRMVIPKNLPDQDIRIKIACRLDKPLNMKHCGYKEKKSEPSEMMQLDGYTVDYIEAASANLMFGIDL\n+# NGGRFFFNAVREGDSISFACDDENECSLWVMAMYRATGQSHKPTPPITQDKNSAMSKIQGARVAPDGSIFLWASFFVAAATRNSSSYHWFRVGGRLNP\n+# MVVSAAARMEWDMCAQSPLASTWRGIGWWSSSERGQPYDLVDVEVPKSGATHYHVSCRGEVNQPETVVRDGLMEAESTDGGVKDAFATELCVEVPEDK\n+# LHVVVWGWFSPGQVFVLDEYCARYGVRGCYRHLCYLSDLLDRAEKQHMIDPTLIHYSFAFCASHVHGNRPDGVGSITHEEKEKFSEIKERLRQLLEFQ\n+# ITNFRYCFPFGRPEGALKATLSLLERVLMKDIVTPVPPEEVRQMIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVP\n+# GKAYRKGPREIPSDIQDLRGEVIVPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASA\n+# ASTNGSSFRYYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKM\n+# MAVDMIEQCIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLS\n+# KLARYDEGSLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDF\n+# ELQGVLEDKLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVGNLLGKGIGGLS\n+# SKLGSGSWF]\n+# end gene contig70.g117\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/galaxy/galaxy/database/files/000/dataset_2.dat --UTR=off --genemodel=complete --species=fly\n'

diff -r 000000000000 -r f493979f1408 test-data/augustus/hubaInputs/GTF/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustus/hubaInputs/GTF/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,66784 @@\n+>contig1\n+AAAACTAATTTTATCAAAATCGGACAACTATATCATATAGCTGCCATACG\n+AACGATCGGAAAATTGGTAAGTAAATAATTAAAAATATTATATCTTTGGT\n+GTGTTTTTGGAAATAACATTTTTTAATATGTTTTGAATTTTGAATTAAAT\n+TCTATCAAAATCGGACGACTATATCATATAGCTGCCATACAAACGATCGG\n+AAAATTGGTGAATAAATAATATGAAAAAATTATATCTTTGGTTATTTTTT\n+AGACAAATAACCTCCAACGCTTGGAAATAACATTTTTTAATTAGTTATAA\n+ATTTGATATTTTAATTTTATCAAAATCGGACGAATATAGCATATAGCTGT\n+TAAAATAATATGAAACAAATTATAGCTCCGGTGTTTTTTACATATTATCT\n+TATACTATTGGGAAAATAGTTTATTATATTTTAAAGAATTTCCAATTAAA\n+CTCTAACATATAGCTTTCAAAGAAACGGTCAAAAAAGTAAAGAAATCATT\n+TTTTTTTAACATCACTGAAGCTAGAAACAATCCTTAAAAATGTAACATGG\n+TGTTAGTAGCATTGAAAATTGCTTATAACTGCAAAGGGAAAACAAACATC\n+GGCTTGCCGAATGTAATTTCCATTCTTGTTTGACTTGAGTTTATAACTTA\n+CAATTATGGTAAGGTGCCTGATTTTGGTTTTTGCCATACGGTATGTGGTA\n+GTTATCATTTTGCCGTGCTATAAGTGACATCACAGCCGATTCTTTTACTC\n+CATAATGGGCCAATGTGTTGAGGCGTTTCCATCCATTTATTGTTTTTGTA\n+GTTAGGTCTTCATCTTGTAATGTGAGATGACCTCCTCTTCCATGCCTCCA\n+TTCTAAGTCAACTTCGTGCACAGATGGTCTCATAGAAAACGGAGTATTTT\n+TAAAAATTGCGTCCAAAATTTTTAATTTAACTTGCGATATGGTATCCAAA\n+TCGTTTACACGACATTGGACTTTTTCATCAAGATCATCTTGTAAAATGTG\n+CAAAATTACAACAGAATGGGTAACTTGTTCGTGGAGAAGTCGTTCCTCTG\n+AAAGTGAATAACGAGCATCGTGGGTTATTGCGTCCACCAAACCCTTTTCA\n+ATTTGATGCTTAATTGCCTTGAACAGCAAAAATAAATTAGATCCAGCATA\n+TTCTTTTAGGTAGTCGTACATACAAATTGCTAAGTAGTTTGTTAACATTT\n+TTTCAACTACGCTCTCAGTGCGTCGTAGCATTAGCTGAGGATGCTTGCTG\n+GCGAGCGATTTGTCAATTAATCGCAATAAAAGGGACTTTAAAATTTCCGT\n+CGCATATTCCATTTTGTTCATTAGAACAACCATAAGTAAAGAGGCGACGT\n+TAACTCGATCGCGAATTGAGAAAGATGACCGTTGAGCTTCTAAAGTTTCT\n+ATGAACAATAGTAAAAAATATTTGTTTCCAATAAGTTGCTCGAATTGTAT\n+CATAGCTGCATCATAGTTAGTGTGCGGGCTACTTCCACAAAATTTTCGGG\n+AGTTTAGAATAGGATGATCTGATACACCGGGAAAGAAAACTTTCATAATG\n+TAATTGACGTGATCTAACGTTGGTATACCGGTGCTCTCCAAATCTGCTGT\n+TAGATCGGTCATGTCCGTTTGGAGCTCAGCAAATGCCTGTTTACACTCAG\n+AACGAACGTTGCTTTCCAATGTTATCATCTGTATCTGAATTCGTTTGTAT\n+TCCCGTTCTGCTTGGGTCGATTTCCTTCTAAATATTATTAGTACGACAAC\n+CAAAACGATGACAAGCACTGCAACTGTCAATATAACGACAAACATGGCAT\n+GTGAAAAAACATAGGGTTTATTTAAATCATATTTCAAATATCCTATGGCG\n+AAACGAAGATTTCGCCCTACTTTAACCACAACTAGAGGTAAATCTGTCGA\n+TTGATCCACACCATTTTCATCAGTTGGGAGTGGTTGATGTTCCGGTGGAA\n+TGCACAAAAGTTGAGTTAGTGTAAGGCTTGTTATATTGCATTGAGTAGTA\n+CCAATGGTTACATTAACGTCGTATTCATCAGCTGCCAAATTTAGTAGCTC\n+GCCTTCAATAACCAAGCTGTCACCCTTGTATAGTTTAATTCCGTCATTTG\n+GAAATGGTAAATATTTTGGATCGGCTAAATAAACAATAGTGCTCCTGATA\n+TCATGAAAGTATTTATTTAGATCTCGAACAAGCTGTACATTGTCCATTAC\n+AAAACTAAGTTGTAAATTCAGTTGCGTTTCATGGACCTTTACAAAAGTTG\n+TAACATCCATATTATTATTGACGAAATAGCTAGGCGCAGTTCCCCCTGTT\n+GTGTATATATGAAAGTTGTCTACGAAGTCTGCTTTTCGCTTTCGTCTAGA\n+ATATTCGTTCTGATGCGCACTTTCATTTTTAAAGTCAAATTCCGAATCCA\n+TCACTCTGTTAGAACTTTTAAATGCTTGAAATTTATCATTTACCGGAGGA\n+GATGGGCATTCCATTTGATTTGAATTGATTACTACGCAAGATGTTTTGTT\n+TACTCTTTCATTATCAAAAAAAACTTCAAGTTCAGGCTTTTGAATTGAAT\n+TAAGATACATTCCATGAACGGTCAGAACGCGACCACCACTTACAAAACTG\n+CGTAAAGGCTTAATCTGCATTATACGCGGGTCTTGGGTATAGTTAAAAAT\n+AGAACAGGGCTGCCTTGGTAACGTACGAAATTGGTATGAACCGAAATTAC\n+TTCGAGTTAGATTTTTATTGGGTATAGTTGCGGGTGAGATATGACATTCT\n+AAAGTTCGGTTGGCACCGTCAATAAGAAGGTGTAGAGACCGTATTGGTTC\n+TGGCTGGGTCGCCTCTGATGTAGTACTACTAACTTGAGTTGAAGAAGCTT\n+GTGTAACGTTTATATGACACTCGTACTCATCTAAATATGCTCGCATGGTT\n+GATCCAATGTTCAAAAACTTTCCTATTAACGACAATTGTGTTCCTCCCGA\n+CCTGGGCCCAATCGTGGGATATAATCCTGTTAGCAAAACATTCTTAAAGT\n+GAAATTGTACACTAGATTCAGTATACCCTGCATCATTTGCAACCTTTATA\n+GGCGCTGACATTTCATACATCACTGCTCCAGTGCGGCATTCGATCTTTAC\n+AGAAATTTGGTAGTTGACTAGTTCACAAGGCACAGACCCAATAAATATTT\n+TTCCACGCACATCTCCTTCGCGAATGCCCAAATTACTGCCTTCAATTGTA\n+ATAAGGGTACCACCCTCAATAGGTCCAGATAACGGTTTAATAATATCGAT\n+CCTTGGTAAAGGGCACTCGTTTTCTTTAGTTGTTTTTGATCCTGCACTAA\n+TAGCACGATCACTGTCTGCTATGCAAGTCTCGTTATATACACATGAGTTG\n+CTGCACCAAGCACATTGGTATTTTGGATCACGAGTGACACACAAACTGCA\n+ATCAGCATGATCCCGATGTGAGCCCAGTACGTCGCATTTATATAATGTAA\n+CAATCGCCGTGTCCACATAGTGCTGGAAATTCCATGTAATTACAACCTTT\n+GCTTGGTATTCATGTGTATTAGTCTCGTAGAAATAAGGTGTTTTTTCACA\n+AACAACAATCTTGTTTGACTCAATGTGGGCAGGCAATAGCATCTGAGCAG\n+CTTCAATATGAACTGTACACAAGAATCCAGCGTGAGCGCTTTTGGGTTTT\n+GGTAAGTTTTCTATCTCTAAACGAATTTCTTTTGGCACCCGCACCGGTAA\n+AAGAATCGCCGGACGATTGCTTTTTAAATGGGGGCATTGACCAACACTAG\n+TTACCGAATTTTCTATATTACGACATTGTATTGATTGATGGACACATTTA\n+TTGTCAAAAATACACC'..b'CCACTGGACCCGTTGGATAGCGTC\n+GGCACTTTTCTGTTTGGTGCCATTCACTGGTCACTAGTAGGACCGCTCTG\n+CCTATTAAAATAGGAGTGCTGCTTAGAATTTATTTCAGCAAGACAGCCGT\n+AAGATATATATGAATAGTATTTAACGGCAGTGGCAGAGGCCTTTACAATA\n+TAAGGCTTTACGGGATTTTAAACAATGAAAAACAAAAATATTTTTATAGA\n+GTCGAGATAAAATACTTTTTACAATAAATACTAAGTATTTTTAAAAGATA\n+AAAATATTTAAAAGTAAATACTGAATATTTTAACAGGTGTTAAGTACTGG\n+GAACTGTGACTAAGGACGGCGGTATATCGCTACCATAATATTTTTAAAGG\n+AACTGAATACTGAAAGATGTGACCAAAATGGTAGAATATCGCTAACGAAA\n+ATCACAGACGCAAATATCGATAGTGGCCTAGAGACCCGATATCGCCGCCG\n+TGATTATCGATGAAACTACAGCTGAGCTGCTTGTTTACATTCTAAAGTTA\n+AAATTTTTAAAAATTTCCAATACAAAAAAAAATTCTTCGTATTAACACGG\n+CTGTTTGCCGGTAAGATCTGAAGTGGATTCAAGTTGCAGCACCCTCAGGA\n+AAAGAATAAATTATTATAATATAATAATATAATATAAAGAATTTAAATTC\n+GAACCAAACGCGGTATGTCACTCTTCATTTAGAGAATTTGTGGCTTTGTT\n+TTGTACAAAAAACTATTCTTTTTTCTTGAAAATTAGCATCAAGAATTTAT\n+TGCCAAAACAGAACGCAATTCTGCTAAATCTGGTTACCCTGCCAAATGGC\n+TGGCCGTTCTGTGCATTCAATAACACAAGCTAACGGCTTACGGCACATTC\n+GGAAAGATCCAAAAGAATTTCTATTCCGGCATTTTTTATGTATTATCGTC\n+CAATTTTTGTATGTGTATTCATTCTTTTGGCTGTCCGTTATTAAGCTTTT\n+CTTATCCACATAAGCTGACCAGCTGCCAAAAAGCCGACCGTTTTGTGCAG\n+CCAATAACCCAAGCTAACTATCAACAGCAATTTCGAAAAATCCAGAAGAA\n+GCTATCCTTCGGCAATTTTTTCTTATATTATAATTTTTTTGTCACAATTT\n+TTTGTCAAAAAATCGACAATAATTAAGTGTTTACATTTTAATGCGATTTA\n+ATTGGAAATTTGAATTCGAATCAAACGCGGTGTCACTCTACATATGGACA\n+ATTTGTGGCTACAAAATTAGTTGAAAGTGCATGTTTTTTTTTAAGTGAAA\n+TAAAACAAAAACAGCAATAACAGGCCAAAATGTTGTTTTATAAATAAATA\n+CTTACATATCCGCATATAAATATGAATGAAAAAAAAAACAGCAAGACTGG\n+GCCAAAATATTGTTCTTTAATATGTAAATAAATACATATCTACATATACA\n+TATGTGGACAAAAGTGTTAAAATTAGTTAATAGTGCATGTTTTTTAAATG\n+AAAAAATAAAACAAAAAAAGCAAGCAAATATAAATTATATTCCACACACA\n+TTTACAATAATTTCAAACTACGCTAAAAATACCCAACAGAAAAAACATAG\n+AAAGGTAAACAAAATACAAGAATATCAAAAAAAATCTAATTTTCACGTTG\n+TTGTGGCCGGTACCACCGGTCATACATACATATAGATACATATTTAGATT\n+CTCACAAAAAGAATAGAAAATTACCGCTAATTTCCTTATATACGTTTTTG\n+TTTTCAGTGTTTTGAAATAGTATTTTTCAAACAAAAAACAATACAAAAGG\n+GTTAAAAAAATTGTTCGATTGGCTTTAACATACTAATTAAAAAAAATCAC\n+AATTTTTTGGCAAAATATCGAAAAAAATTAAGTGTTTACATTTTTATGCG\n+AATTATTTGGAAATTTAAATAAGAACCCAACGCGGTTTGTCACTCTACAT\n+ATGGACAATTTGTGGCTTTGTTTTGAACAAAAAATGAATTTTTTTTTACT\n+CAAAATTAACAAGAAGAAACAGTAATGCGGGTTTTGATCGCAATTCTGCT\n+AAATCGAATTTCCGTGCCCAAAGGCTGACCTTTTTGTGCAGCAAATAGCC\n+CAAGCTAATAATCTACAGCAATTTCTTAAAGACCGAAAATGTATCAACTT\n+CGGCAAAATATGAAAATTTAACATTTATTTTTCAACATTTTTTGCCAAAT\n+AATCGACAAAAATTTCAGTGTCCCGATTTGGATGCGAATTAATTGAGGAC\n+AATTGTGACTTTGTTTTGTAAAAAAACTATTTTTTTTACTGAAAATTACA\n+ATCAAGAATCTAAGGCCAAATCAGAATATTTTCACTGCGGTTTTTTGATC\n+GCAATTCTGCTAAATCGGGTTCCGTGCCAAAAAGCTGACTATTTTTTTTA\n+CTGAGAATTAGCATCAAGAATTTATTGCCAAAACAGAACGCAATTCTGCT\n+AAATCGGGTTGCCCTGCCAAAAGGCTGGCCGTTTTGCGCATTCAATAACA\n+CAAGCTAACGGTTTACAGCACATTCGGAAAGATCCAAAAGAATTTCTATT\n+TCGGCATTTTTTATGTATTATCGTCTAATTTTGGTATGTGTATTCATTCT\n+TTTGGCTGTCCGTTATTAAGCTGCTTTTCTTATTCACATATTCAATGGCG\n+CAGTACATAAAAAGAATGAACCGTGGTTTTCTTGCCCTCTCCATCTCCCT\n+CTACCACTTCCCCTCTCAACAACTATCTCACGCACTCTGTCCCTTCTCGT\n+CTCTGTCACCCTCTCTTTACCTACCTCACTCTGGCACACTCTCTCTACCT\n+ATCTCACTCTGTCACCTTCTTCTACCTAATTCTCTCTGTCGCGCTCGCTC\n+TCTCAACATGCCTTTCGCACCGTATCTCTTCGTTTCTCTGTATGCTTGCT\n+CTCTTAATTTAAGTTTCTCTTTCTTTGTGTTCAATATCTTTCGCGCTCGT\n+GACTCCTATTGACCGGACTCTGAGCGGTGCTCATTAAGAGTGGAGTTTTC\n+GATGATGGCGGGTGGCGCGAACGAGAATTTTTTACATAAAGGTAAGTTGC\n+CAATTCTTTTTTAAATGTGACATACAGCATGCATATTTTATTTATTGTAA\n+TTATATGTGAAAGAATAAAATTATATGTACTTTTATCTAATCTATTGCAT\n+CTATTTTTTCACAGGTAAACGAGTCACACGAGAAGTAAAACACAAACACA\n+AGGATCAAAATAAAATTCAGGTGAGTGAACGAACGTGTTGAAAGTAGTTA\n+ATAGTGCATGTCTATTTAAGTGTAAGAAACAAAAAAGACACAAATGGGCC\n+AATAATTCGTTTCTTTAATAGATAACTGCCTATATTATGTTCAAACTATG\n+CTAAAAAGACCCAAAAGGAAAACATAAAGTATATACCTTGCAAAATGAAT\n+AAAAAGAAATCATATATATTCATATACGTTTGACCGGTACCACCGGTCAT\n+ACATACATAAACATAAACACAAAAAGACTAGAATATAAATACCATATTTT\n+TGATTGGCTTAAAAATGGCACAAAAAAAAGATAAAAACTAGAGTGTCTAG\n+CTTTAAGTGACAATCGACTCGGAAAATGATCAAGAAATAAATGAAAAATT\n+TGTCTTGCGGCTTTTTGGTCGCAATTCTAAATCGGTTTGTATGTATGTCA\n+CTCTTCATGTATACAATTTGGTGGCTTTGTATTCCACAAAAGTCACAGTA\n+GTCACAAAAGTTTTTTTTACTGAAAATTACCATCAAGAGTCTATGGCCAA\n+ATCAGAATATTTTCACTGCGGTTTTTTATTTCAATTCTGCTAAATCGGGT\n+TTCCGTGCCAAAAAGCTTTTGCAGCCAACAACAATATTCAATTTTTTGGC\n+AAAAAATCGACAAAAAAATT\n'

diff -r 000000000000 -r f493979f1408 test-data/augustus/output/augustusDbia3.bb

Binary file test-data/augustus/output/augustusDbia3.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/augustus/workflowInputs/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustus/workflowInputs/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/augustusDbia3.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustusDbia3.gff3 Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,9513 @@\n+##gff-version 3\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/galaxy/galaxy/dependency_dir/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# human version. Using default transition matrix.\n+# Looks like /home/galaxy/galaxy/database/files/000/dataset_2.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+contig1\tAUGUSTUS\tgene\t641\t23169\t1\t-\t.\tID=contig1.g1\n+contig1\tAUGUSTUS\ttranscript\t641\t23169\t.\t-\t.\tID=contig1.g1.t1;Parent=contig1.g1\n+contig1\tAUGUSTUS\tCDS\t641\t5409\t.\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t13455\t13545\t.\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t17461\t17543\t.\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t23019\t23169\t.\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tstart_codon\t23167\t23169\t.\t-\t0\tParent=contig1.g1.t1\n+# coding sequence = [atgcacattcagttgtctactctcgcctttcaggttcagactgcagatgagttcgtcgtcgatgcgcgtgatagacgat\n+# ccttcatccagcgcaggtgtcgacctgcgaattctctccgtacagcgtcacgggaagaatccggaataggagctgtaggtgttgctgataaatgtagt\n+# gcggatgcagaagttttaccgctgcattttgttggtgcgccaggttcgaaactgatgtcgagtcatgcaattgcttttcctataagtagccgagaatt\n+# gaacttacagatatctctaagatttttaatatttgcttacgaatacgctagcgcatgcgaaatttacagccttccgcggtttccatcaacgcctcaat\n+# ttgtcgcagttccattggcggctaatgatgaaaatgcatcaacatatgcatttgtaggtcctgcacgatattcatggaaagaagaggatattttatat\n+# gtgggaacgacgttcacgaacgttggtgattatcgccatgacgttcctgccatttcgtcccgtcggcttgatgatttaaactacgcagagttttcaat\n+# acagcagtcaattataaatatcgatgtcaaatatcgggatcatttcttagtcgattatgtttatggctttaactcttctgaatatgcgtactttgtta\n+# ttgttcaaaaaaaatcacatttagctgatgaggcaggttatgtaacccgtttggctcgaatatgtattacagatcccaattatgacagttatactgaa\n+# ataacagttcagtgtacggccactgaaaatcatattgactacaatatactacgcgatgccaaagtaactccggcaagccaaaaattagctcagaaaat\n+# gggtataaaaaaggacgatcacgtgttagtaactgttttttcgccctcgaaagagataagcgatcagccagaaagcaaatcggctatgtgcatatata\n+# gcataaaagacattgaggacatgtttattgaaaatattcatctgtgctttaacggaaccataaaggatagaaatttgggttatatatcgggcactatc\n+# aatgacggccggtgcccaatagttggctcgctcggtaacatatacaacttttgttctgtaggacttaagataagcggagtttctcctatcactacaca\n+# cgctctctttcattttgataatgtatcagttacgtcaataactgcaacgtcaacgactgatcagcagcattctcttgcttttcttggaaccgacaagg\n+# gattgataaaaaaagttttattatctggtcagaatccaggtgagtacgaagaaatagttgtggatgctggaaatcggatactaccaaacactatgatg\n+# tcgcccaaaaaagatttcctttacgttttatcgcaacgtaaaataactaaactcagaatcgagcattgttctgtatacacaaattgttcagcttgctt\n+# ggagtctcgggaccctttttgtggatggtgttcattggaaaaacggtgcaccgtgcggtcaacatgtcagcgagatacgtcagcatcgcgatggcttt\n+# ctttgggcagtgggcaacagtgtattgagtttgaatcaattatccctgagaaaataccaattactgatctaacacacctgcacctaataattcgaaca\n+# ctgcccgaaccttttaatgcaaaataccgatgtgtctttggaaactctacccctattgacgccgaaatcctggacaatggactcggatgtgctacccc\n+# cccactagatgaaagaccagtaataccaactaatacagaccatgttttggtgccattgtccgttagaagttcagagacaaataaggactttgtatcaa\n+# gattttttgcattctttgactgttcgcatcatggaaattgccaggaatgtttacaaagttcatggggctgcaactggtgtatttttgacaataaatgt\n+# gtccatcaatcaatacaatgtcgtaatatagaaaattcggtaactagtgttggtcaatgcccccatttaaaaagcaatcgtccggcgattcttttacc\n+# ggtgcgggtgccaaaagaaattcgtttagagatagaaaacttaccaaaacccaaaagcgctcacgctggattcttgtgtacagttcatattgaagctg\n+# ctcagatgctattgcctgcccacattgagtcaaacaagattgttgtttgtgaaaaaacaccttatttctacgagactaatacacatgaataccaagca\n+# aaggttgtaattacatggaatttccagcactatgtggacacggcgattgttaca'..b'=contig70.g235\n+contig70\tAUGUSTUS\ttranscript\t24505\t50605\t.\t+\t.\tID=contig70.g235.t1;Parent=contig70.g235\n+contig70\tAUGUSTUS\tstart_codon\t24505\t24507\t.\t+\t0\tParent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t24505\t24577\t.\t+\t0\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t27274\t27411\t.\t+\t2\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t28524\t28636\t.\t+\t2\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t33015\t33225\t.\t+\t0\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t38419\t38560\t.\t+\t2\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t45726\t46035\t.\t+\t1\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t46098\t46478\t.\t+\t0\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t46932\t47068\t.\t+\t0\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t47124\t47263\t.\t+\t1\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+contig70\tAUGUSTUS\tCDS\t50403\t50605\t.\t+\t2\tID=contig70.g235.t1.cds;Parent=contig70.g235.t1\n+# coding sequence = [atgattaaaaaaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcactt\n+# ttccgttcaagggacacgtgccagggaaatcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctat\n+# cggaaaggtcccagggaaatcccgtcggatattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagc\n+# agaactttgtgttgatctgttgcaacaaaatgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatg\n+# atgatgtaccaaaaggccacaatgaaagcgatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaat\n+# ggatcgtcatttcgttattgtatgccgacacatgcagtatacaccacgccagtaccaacggcatataatttgaggaatgggcgttttcatcagcacct\n+# gcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcataagggatttgaaaaagaacgctggg\n+# aaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataagagacctgcactggccagacgcagag\n+# tttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactgattcgtcttttcagtcgtggctaaa\n+# aaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattagatgctaaaaatcaaagctttaaat\n+# tgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgtagctatgacacaaggtctaactggt\n+# aaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgattcttagttttacaaatgtatcgag\n+# ctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattggcgacgatttatggaccctgaatt\n+# tctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctgcactacgctcaagtttcatctatt\n+# tctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagcatatcaagcagtcgcacagcgaat\n+# ggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgagaaggggaagaagaagatactggcg\n+# acgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttaccaacgttgttgccggccgtgtggca\n+# accggaacatcaccagcaggtagtgccacattaatccgccttgaccagcaacaacaagagcgatacagacggcagcaggatcagttgcacgatgagca\n+# gcaagaaagccatgcccgacaaaagcaggaacttgctcttgcatcttacaccccagggacggtcgtcaatggattgggtcaatcatcagtcacggcaa\n+# gttag]\n+# protein sequence = [MIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVPGKAYRKGPREIPSDIQDLRGEVI\n+# VPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASAASTNGSSFRYCMPTHAVYTTPVP\n+# TAYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKMMAVDMIEQ\n+# CIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLSKLARYDEG\n+# SLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDFELQGVLED\n+# KLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVATGTSPAGSATLIRLDQQQQ\n+# ERYRRQQDQLHDEQQESHARQKQELALASYTPGTVVNGLGQSSVTAS]\n+# end gene contig70.g235\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/galaxy/galaxy/database/files/000/dataset_2.dat --UTR=off --genemodel=complete --species=human\n'

diff -r 000000000000 -r f493979f1408 test-data/augustusOutput.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/augustusOutput.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,1 @@
+<html><body><p>The following generated by Hub Archive Creator:</p><ul><li><a href="./myHub.zip">./myHub.zip</a></li><li><a href="myHub/dbia.html">myHub/dbia.html</a></li><li><a href="myHub/hub.txt">myHub/hub.txt</a></li><li><a href="myHub/genomes.txt">myHub/genomes.txt</a></li><li><a href="myHub/dbia3/dataset_7.2bit">myHub/dbia3/dataset_7.2bit</a></li><li><a href="myHub/dbia3/groups.txt">myHub/dbia3/groups.txt</a></li><li><a href="myHub/dbia3/trackDb.txt">myHub/dbia3/trackDb.txt</a></li><li><a href="myHub/dbia3/description.html">myHub/dbia3/description.html</a></li><li><a href="myHub/dbia3/tracks/augustusDbia3.bb">myHub/dbia3/tracks/augustusDbia3.bb</a></li><ul></body></html>
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 test-data/bam/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,20 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat
+DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x17c0b50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/904/dataset_1272_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/bam/bam.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/bam.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,73 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/bam/inputs/HISAT2_Accepted_Hits.bai

Binary file test-data/bam/inputs/HISAT2_Accepted_Hits.bai has changed

diff -r 000000000000 -r f493979f1408 test-data/bam/inputs/HISAT2_Accepted_Hits.bam

Binary file test-data/bam/inputs/HISAT2_Accepted_Hits.bam has changed

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/Dbia3/Dbia3.2bit

Binary file test-data/bam/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track HISAT2_Accepted_Hits.bam
+    longLabel HISAT2 Accepted Hits.bam
+    shortLabel HISAT2 Accepted
+    bigDataUrl tracks/HISAT2_Accepted_Hits.bam
+    type bam
+    visibility pack
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam

Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai

Binary file test-data/bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/bam/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,32 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1199.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'TBLASTN_Alignment_to_proteins', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpmC5L13.sortedBed
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmphIusrY.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/905/dataset_1273_files/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb
+DEBUG:root:typeOption: None
+DEBUG:root:autoSql: None
+DEBUG:root:tab option: False
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bed.Bed object at 0x2cbbd10>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/905/dataset_1273_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track TBLASTN_Alignment_to_proteins.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/bed_generic.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/bed_generic.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb">TBLASTN_Alignment_to_proteins.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,40 @@
+contig2 16199 18659 ci-PA 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 18939 20598 ci-PA 604 - 18939 20598 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig2 18712 18877 ci-PA 964 - 18712 18877 0 1 165, 0,
+contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0,
+contig24 12402 12561 ci-PA 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12570 ci-PA 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig23 32405 32564 ci-PA 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32573 ci-PA 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig67 20513 20759 ci-PA 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20531 20753 ci-PA 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,
+contig67 18177 18309 ci-PA 0 - 18177 18309 0 1 132, 0,
+contig67 20471 20660 ci-PA 0 - 20471 20660 0 1 189, 0,
+contig66 35516 35762 ci-PA 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35534 35756 ci-PA 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig66 33180 33312 ci-PA 0 - 33180 33312 0 1 132, 0,
+contig66 35474 35663 ci-PA 0 - 35474 35663 0 1 189, 0,
+contig2 18711 20598 ci-PC 584 - 18711 20598 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig2 18601 18889 ci-PC 0 - 18601 18889 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig2 16199 18659 ci-PB 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 18939 20268 ci-PB 560 - 18939 20268 0 4 510,210,432,51, 0,564,774,1278,
+contig2 18712 18877 ci-PB 964 - 18712 18877 0 1 165, 0,
+contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278,
+contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0,
+contig24 12402 12561 ci-PB 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12570 ci-PB 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig23 32405 32564 ci-PB 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32573 ci-PB 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig67 20513 20759 ci-PB 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20531 20753 ci-PB 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,
+contig67 18177 18309 ci-PB 0 - 18177 18309 0 1 132, 0,
+contig67 20471 20660 ci-PB 0 - 20471 20660 0 1 189, 0,
+contig66 35516 35762 ci-PB 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35534 35756 ci-PB 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig66 33180 33312 ci-PB 0 - 33180 33312 0 1 132, 0,
+contig66 35474 35663 ci-PB 0 - 35474 35663 0 1 189, 0,

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins.bed Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/Dbia3/Dbia3.2bit

Binary file test-data/bed_generic/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track TBLASTN_Alignment_to_proteins.bb
+    longLabel TBLASTN Alignment to proteins
+    shortLabel TBLASTN Alignme
+    bigDataUrl tracks/TBLASTN_Alignment_to_proteins.bb
+    type bigBed
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb

Binary file test-data/bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/bed_generic/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_generic/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,32 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/000/dataset_285.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Repeating_Elements_by_TrfBig', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpJsUz0x.sortedBed
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpPbCGNa.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/923/dataset_1291_files/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb
+DEBUG:root:typeOption: bed4+12
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/trf_simpleRepeat.as
+DEBUG:root:tab option: False
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<BedSimpleRepeats.BedSimpleRepeats object at 0xee8d10>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/923/dataset_1291_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Repeating_Elements_by_TrfBig.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/bed_simple_repeats_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb">Repeating_Elements_by_TrfBig.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,602 @@\n+contig1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+contig1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t540\t590\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig2\t1094\t1135\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig2\t8220\t8316\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig2\t8284\t8353\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig2\t9033\t9066\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig2\t13992\t14461\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig2\t22404\t22439\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig2\t23269\t23324\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig2\t23269\t23324\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig2\t23269\t23324\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig2\t27949\t28001\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig2\t38280\t38311\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t3265\t3296\ttrf\t16\t1.9\t16\t93\t0\t53\t41\t19\t6\t32\t1.77\tTACATACATACATATG\n+contig3\t17933\t17958\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig3\t19067\t19124\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig3\t23368\t23418\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig3\t24889\t25322\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig3\t26816\t26900\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig3\t26816\t26887\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig3\t26816\t26900\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT\n+contig3\t26820\t26887\ttrf\t17\t3.7\t19\t80\t20\t74\t20\t4\t0\t74\t0.99\tTTTATATATTTTTTTTTCA\n+contig3\t29468\t29515\ttrf\t25\t2.0\t23\t84\t12\t60\t34\t0\t17\t48\t1.47\tATTATAATTATGATGTTATGATG\n+contig3\t38756\t38791\ttrf\t10\t3.6\t10\t92\t7\t63\t40\t0\t0\t60\t0.97\tATTTATTTAA\n+contig3\t38758\t38788\ttrf\t9\t3.2\t9\t95\t4\t51\t40\t0\t0\t60\t0.97\tTTATTTAAA\n+contig4\t7931\t7956\ttrf\t10\t2.5\t10\t100\t0\t50\t60\t8\t0\t32\t1.26\tATATAAACAT\n+contig4\t9065\t9122\ttrf\t28\t2.0\t28\t100\t0\t114\t43\t14\t10\t31\t1.79\tAATTAAATTTTATCAAAATCGGACGACT\n+contig4\t13366\t13416\ttrf\t2\t25.0\t2\t100\t0\t100\t50\t0\t0\t50\t1.00\tAT\n+contig4\t14887\t15320\ttrf\t160\t2.7\t161\t80\t6\t452\t36\t12\t12\t38\t1.82\tAATATTAAAAATTATATCTTTGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTATTTGGTTTAATTTCGAATTAAATTTTATTAAAATCGGACGACCATATCATACAGCTCCCATAGAAACAATCGGAAAATTAGTCGGAAACATG\n+contig4\t16814\t16898\ttrf\t18\t5.0\t16\t83\t13\t89\t20\t5\t0\t73\t1.03\tTTTTTTTATATATTTT\n+contig4\t16814\t16885\ttrf\t18\t4.1\t17\t84\t12\t90\t19\t4\t0\t76\t0.96\tTTTTTTTATATATTTTT\n+contig4\t16814\t16898\ttrf\t15\t5.2\t15\t79\t16\t71\t20\t5\t0\t73\t1.03\tTTTTTTTATATATAT'..b'\n+contig69\t18503\t18850\ttrf\t163\t2.1\t163\t88\t3\t502\t36\t12\t16\t35\t1.86\tCTTTGGTGCTATTTGACATATAACCTCCTAAGCTTGGAAATATCATTTTTTAATTGATTTTGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAG\n+contig69\t18536\t18888\ttrf\t163\t2.2\t161\t85\t4\t472\t36\t9\t16\t37\t1.82\tTTGGAAATACAATTTTTTATATTTATGAAATTCAAATTAAATTTGATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACGATCGGAAAATTGGTGGAAAAATAATATGAAACAAATTATAGCTTTGGAGCTGTTTGACATATAACCCTATAAGA\n+contig69\t19781\t19812\ttrf\t15\t2.1\t14\t94\t5\t53\t58\t0\t0\t41\t0.98\tATATAATTATAATA\n+contig69\t23637\t24060\ttrf\t162\t2.7\t156\t83\t6\t496\t37\t11\t12\t38\t1.79\tAAAAAAATTATATCTTCGGTGCTTTTTAACATATAACCTTCTAAGCTTGGAAATAACATTTTTTAATTAGTTCTGAATTTCAATTAAATTTTATCAAAATCGGACGACTTATAGCTGCCATAGGAACGATCGAAAAATTGATGGGAAAATAAATAT\n+contig69\t36863\t36892\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig69\t38645\t39124\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig69\t43653\t44084\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t6910\t6939\ttrf\t15\t1.9\t15\t100\t0\t58\t27\t20\t48\t3\t1.66\tGGGGAACGCGAGCAT\n+contig70\t8692\t9171\ttrf\t158\t3.0\t157\t85\t5\t615\t34\t13\t13\t38\t1.84\tTAAAAATTGTTATTTCCAAGCTTAGAAGGTTATATGTTAAAAAACACCAAGATATAATTTTTTCATATTTTCCGACTATTTTTCCGATCGTTTCTATGGCAGCTATATGATATAGTCGTCCGATTTTGATAAAATTTAATTTGAAATTAAAACCAAT\n+contig70\t13700\t14131\ttrf\t162\t2.7\t162\t87\t4\t586\t40\t10\t13\t35\t1.79\tAACATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGAAGACTATATCATATAGCTGTCATAGGAACGATCGAAAAATTGGTGGAAAATAATATAATAAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t17962\t18295\ttrf\t161\t2.1\t160\t83\t5\t413\t37\t12\t13\t35\t1.84\tAAAAAATTATATCTCTGGTGTTTTTAAACATATAACCTCCTAAACTTGGAAATAACATTTTATAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAACCCGACGACTATATCATACATGTAACTGTAACGATCGGAAAATTGATGGGAAAATAATATG\n+contig70\t19030\t19306\ttrf\t137\t2.0\t137\t94\t1\t482\t39\t13\t13\t34\t1.83\tTTTAACACATACCTTTCTAAGCTTGGATATAACATTTTTAAACTGGTTCTGAATTTCAAATTAAATTCAATTAAAATCGGACGACTATATCATATAGCTCCCATAGGAAAAATCGGAAAATTAGTGAGAAAATAATA\n+contig70\t22269\t22308\ttrf\t19\t2.1\t19\t100\t0\t78\t58\t15\t15\t10\t1.62\tAACTAAGGAAATACCAGAA\n+contig70\t22812\t23252\ttrf\t162\t2.8\t156\t84\t5\t562\t37\t11\t13\t37\t1.81\tTTCTAAGCTTGAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTTAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAAATAAAAATTATATTTGTATTTTTAACATATAACC\n+contig70\t23421\t23486\ttrf\t13\t4.7\t13\t70\t20\t51\t38\t0\t0\t61\t0.96\tATATATATAATTT\n+contig70\t23426\t23479\ttrf\t7\t7.4\t7\t79\t12\t54\t35\t0\t0\t64\t0.94\tTATATTT\n+contig70\t23430\t23486\ttrf\t27\t2.0\t27\t83\t10\t69\t35\t0\t0\t64\t0.94\tATTTATATATTTATTAATATATTTTAT\n+contig70\t25576\t25606\ttrf\t12\t2.5\t12\t94\t0\t51\t33\t26\t36\t3\t1.73\tACGGACGGACAG\n+contig70\t27263\t27382\ttrf\t63\t1.9\t63\t85\t3\t168\t27\t25\t21\t26\t1.99\tATTTTTCCAAGCACTTTCCTGTACAAGGGAAACGTCCCAGGGAAAGCCTATCGGAATTTCAAA\n+contig70\t27353\t27406\ttrf\t25\t2.1\t25\t85\t0\t70\t30\t26\t32\t11\t1.91\tGGAAACGTCCCAGGGAAAGCCCATC\n+contig70\t27848\t27878\ttrf\t12\t2.5\t12\t88\t0\t51\t30\t30\t40\t0\t1.57\tACGGACGGACAG\n+contig70\t35504\t35713\ttrf\t102\t2.0\t102\t99\t0\t409\t37\t12\t13\t36\t1.82\tAAAACGATGGTAGACAAATATGCATATATTTTTTACACAAAACGAAATATAATGGACTTTTAAAAATTCTTTTTTCTATCTTTCCTGGTGGGAGATATATAT\n+contig70\t43333\t43446\ttrf\t57\t2.0\t57\t94\t0\t199\t30\t17\t22\t29\t1.97\tAATATTGGGAATAACATATTATCTTATAATATGGGAGCGCGAAGGCTCCTCGCCCAT\n+contig70\t44242\t44281\ttrf\t7\t5.7\t7\t81\t6\t53\t28\t20\t12\t38\t1.89\tTACATGT\n+contig70\t44241\t44281\ttrf\t13\t2.9\t14\t85\t7\t55\t27\t22\t12\t37\t1.90\tCTACATGTTACATG\n+contig70\t44485\t44531\ttrf\t14\t3.3\t14\t84\t0\t65\t41\t21\t10\t26\t1.86\tAACCGTATATGACT\n+contig70\t45147\t45181\ttrf\t16\t2.0\t17\t88\t11\t52\t52\t0\t2\t44\t1.16\tAAATATTAGTAATATAT\n+contig70\t46706\t46990\ttrf\t147\t1.9\t147\t100\t0\t568\t39\t10\t9\t40\t1.72\tTTCTTTATTTTTTTTATTTTAAAATACTTAGTACTTAGTAATGTCGCTAAAACCAATATAATATTCTTTAAAATTTAGAAAATATATTCAGACTTCGAATTACAAGGTGTATTAGAAGATAAATTAAACTCTAAAGCTTAATTTATC\n+contig70\t53900\t53978\ttrf\t28\t2.8\t28\t80\t5\t97\t15\t43\t5\t35\t1.69\tCTCTGTCACCCTCTCTTTACCTACCTCA\n'

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/Dbia3/Dbia3.2bit

Binary file test-data/bed_simple_repeats/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track Repeating_Elements_by_TrfBig.bb
+    longLabel Repeating Elements by TrfBig
+    shortLabel Repeating Eleme
+    bigDataUrl tracks/Repeating_Elements_by_TrfBig.bb
+    type bigBed 4 +
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb

Binary file test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/bed_simple_repeats/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_simple_repeats/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/bed_splice_junctions/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_splice_junctions/__main__.log Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+

diff -r 000000000000 -r f493979f1408 test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,40 @@
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diff -r 000000000000 -r f493979f1408 test-data/bigwig/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,20 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0xfe0cd0>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/908/dataset_1276_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/bigwig/bigwig.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/bigwig.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/bigwig/inputs/RNA-Seq_Alignment_Summary

Binary file test-data/bigwig/inputs/RNA-Seq_Alignment_Summary has changed

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/Dbia3/Dbia3.2bit

Binary file test-data/bigwig/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track RNA-Seq_Alignment_Summary.bigwig
+    longLabel RNA-Seq Alignment Summary
+    shortLabel RNA-Seq Alignme
+    bigDataUrl tracks/RNA-Seq_Alignment_Summary.bigwig
+    type bigWig
+    visibility full
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig

Binary file test-data/bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/bigwig/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bigwig/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/changed_color/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,20 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat
+DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#8064a2', u'group_name': u'Default group'}
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x2282b50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/918/dataset_1286_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/changed_color/changed_color_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/changed_color_trackhub.html Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/Dbia3/Dbia3.2bit

Binary file test-data/changed_color/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam

Binary file test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai

Binary file test-data/changed_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/changed_color/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/changed_color/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/common/Dbia3.2bit

Binary file test-data/common/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/common/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/dbia3/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,60 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1184.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gff3ToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp7sqcWp.sorted.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
+DEBUG:root:data_value: {u'order_index': u'11', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp66b4It.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpp6ZdZ_.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x1ecae10>, <Gff3.Gff3 object at 0x1ecad10>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
+DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/911/dataset_1279_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/dbia3/gtf_gff_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/gtf_gff_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,73 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/Dbia3/Dbia3.2bit

Binary file test-data/dbia3/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,22 @@
+    track StringTie_Assembled_Transcripts.bb
+    longLabel StringTie Assembled Transcripts
+    shortLabel StringTie Assem
+    bigDataUrl tracks/StringTie_Assembled_Transcripts.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 11
+    color 0,0,0
+    group default_group
+
+    track Augustus_Gene_Predictions.bb
+    longLabel Augustus Gene Predictions
+    shortLabel Augustus Gene P
+    bigDataUrl tracks/Augustus_Gene_Predictions.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb

Binary file test-data/dbia3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/dbia3/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/dbia3/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbia3/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/default_color/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,20 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat
+DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'10', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x2513b50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/917/dataset_1285_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/default_color/default_color_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/default_color_trackhub.html Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/Dbia3/Dbia3.2bit

Binary file test-data/default_color/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam

Binary file test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai

Binary file test-data/default_color/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/default_color/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/default_color/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/gff3/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,38 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1184.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Augustus_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gff3ToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpIyQfQ1.sorted.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpALSFpV.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/909/dataset_1277_files/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gff3.Gff3 object at 0x1804cd0>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/909/dataset_1277_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Augustus_Gene_Predictions.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/gff3/gff3_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/gff3_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/gff3/inputs/Augustus_Gene_Predictions
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/inputs/Augustus_Gene_Predictions Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,6937 @@\n+##gff-version 3\n+# This output was generated with AUGUSTUS (version 3.1.0).\n+# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),\n+# Oliver Keller, Stefanie K\xc3\xb6nig and Lizzy Gerischer.\n+# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\n+# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\n+# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\n+# No extrinsic information on sequences given.\n+# Initialising the parameters using config directory /home/svc_galaxy/new/galaxy/tool_dependency/augustus/3.1/iuc/package_augustus_3_1/24009970003a/config/ ...\n+# fly version. Using default transition matrix.\n+# Looks like /home/svc_galaxy/new/galaxy/database/files/000/dataset_98.dat is in fasta format.\n+# We have hints for 0 sequences and for 0 of the sequences in the input set.\n+#\n+# ----- prediction on sequence number 1 (length = 45179, name = contig1) -----\n+#\n+# Predicted genes for sequence number 1 on both strands\n+# start gene contig1.g1\n+contig1\tAUGUSTUS\tgene\t553\t34688\t0.03\t-\t.\tID=contig1.g1\n+contig1\tAUGUSTUS\ttranscript\t553\t34688\t0.03\t-\t.\tID=contig1.g1.t1;Parent=contig1.g1\n+contig1\tAUGUSTUS\tCDS\t553\t578\t0.41\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t652\t1047\t0.25\t-\t2\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t12541\t12968\t0.87\t-\t1\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t32202\t33826\t0.89\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t33880\t34044\t0.98\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34107\t34619\t0.99\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tCDS\t34674\t34688\t0.45\t-\t0\tID=contig1.g1.t1.cds;Parent=contig1.g1.t1\n+contig1\tAUGUSTUS\tstart_codon\t34686\t34688\t.\t-\t0\tParent=contig1.g1.t1\n+# coding sequence = [atggcagcactctcgcaaaaggactttaatgacggaaaccagagaaatcgtcagaggaaaagtactgtcactgagcagc\n+# cctcatcaacatcaggaagcgtggcccaagtagaagcggacagcgcatcgtcacatttgtctgatcgctgttataacaacatagcaagtactaccaaa\n+# agtattgttggtgatgtgaaaacaagcagacgctgtgaagactttataagtagtggatcagcttcgactccattaaatgaatatgattgtgccaacgc\n+# tgatacgacggatattaaagatgaacctggagattttatagaaacaaattgtcattggcgaagttgttgtattgaatttaatacgcaagatgagcttg\n+# ttaaacatatcaataatgaccatatccaaaccaataagaaggcctttgtctgtcgatgggaaaattgtacccgtggtgaaaaacctttcaaagcgcag\n+# tatatgctagttgtgcatatgcgtcgtcataccggcgaaaagccacataaatgcacatttgaaggctgttttaaggcatattcacgcttggaaaacct\n+# aaaaacacatttacggtcacacacaggtgaaaaaccctatatgtgcgagtatccgggatgcagcaaggcgtttagtaatgcaagcgatcgtgcaaagc\n+# atcaaaatcgtactcacagtaatgagaaaccgtacatttgtaaagctcctggttgcacgaaacgttacaccgacccaagttctttgcgtaaacatgtt\n+# aaaacagttcatggtgctgagttttatgctaataaaaaacacaagggattgcccctaaatgatgcgaactctcgcctccaccgagacagtggccaagg\n+# tcggcataatcttcaagagcataatattgactctagcccttgcagcgaagaacttcaggtgggaaaacttataggcatgtctagtcccagtattaaat\n+# ctgaatctgatgaaagttcaccacatcatcagttgttaagtggagttcgagcttcagactgttttttaacatattcacaagatggtgccgccgaacat\n+# ataactttagatgacggctgggattgtgacgatgacgttgacgtggccgacttaccaattgtcttgcgtgctatggtaaatgttggcagcggaaattc\n+# gatggccccgaccattggagggggtgttgttgcgaggcagcgatttagaagtcgtttgcaaactaaaggaataaactctagtatggttatgcttggca\n+# acatccccgaaagcaatcgcaccattggaataagcgaacttaaccagcgtataacagaacttaagatggagcctggtaccgcttgtgatattacagtt\n+# ccattgaatacggggctggaaaggatttcagaagacttatcacaaaatcaatcaaatataacattaaataagcaaagcttctttaccgcttccggctc\n+# tctccaaggacattttcgtcgcgatagccagaactccactgcaagtacatattatggtagcatgcaaagtcgccgcagtagtcaatcatctcaggtgt\n+# cttctatatctacaatgcgtccaggcccatcgtacaacacaaccacagcttccctctatgatccaatttccccaggatgctctcgacgctctagccaa\n+# atgtctaatgtagtcaactcctacgcacttacatcaacatcaggattgactgcaattaacaaggacttaaatgcaaacagcagcccaaatgcttctat\n+# taataaaccgggtcttggtggtcagtactttggtttttacaataacagtcttcctccacctccatcgtctcatttaattgccaccaatttgaagcatc\n+# tgcaggacacagactctaggagttgttatcacaacacaactggcggtcgattttccattcccaattgtacgccatctctacatttagactacaatgga\n+# ccggctggagagcaggaaattgataaagaaatcccgaataacatattacgacgtcaatctgagccaatgccaaac'..b'ttcgtgttggacgaatattgcgctcgctatggtgtgcggggatgctaccgacatttatgctacctttctgatttactggatcgtgcagaaaagcaac\n+# acatgatagatccaacactaattcactattcatttgcgttttgcgcaagccacgttcacggaaatcgacctgatggggtaggaagcattacgcatgag\n+# gaaaaggaaaaattttctgaaatcaaagaacgcctacgtcagttactggagtttcaaataaccaattttagatactgttttcctttcggtcgccccga\n+# aggcgctcttaaagcgacattatctttactagagagagtgctaatgaaagacattgttacccctgttccacctgaagaagttcgtcaaatgattaaaa\n+# aaagtttagagacggcagcgcttgtaaattacacccgtctctccaataaagctaagattgaaggcacttttccgttcaagggacacgtgccagggaaa\n+# tcctatcggaatttcaaaatttttccaagcactttcctgtacacgggaaacgtcccagggaaagcctatcggaaaggtcccagggaaatcccgtcgga\n+# tattcaggatttgcgaggagaggttattgttccgcccccaaaaaaactagaggacctaattcacttagcagaactttgtgttgatctgttgcaacaaa\n+# atgaagagcactatggagaactgcgcaaacatgacaaaatggataaaattaaaatgcgtaaggaagatgatgatgtaccaaaaggccacaatgaaagc\n+# gatattgatttaaccgccaatactggactcagtagcacatcagacctggcttctgcagcatcaactaatggatcgtcatttcgttattataatttgag\n+# gaatgggcgttttcatcagcacctgcgagacacattcgcaccattagtcgtgcggtacgtggatctgatggaatcttcaatagctcagtcgattcata\n+# agggatttgaaaaagaacgctgggaaagtaaagggaacggatgtgccacctctgaagacttattttggaaactagatgctctacagtcgtttataaga\n+# gacctgcactggccagacgcagagtttcgacaacatttagaacagcgtcttaaaatgatggccgtcgatatgatagagcaatgtatacaacgaactga\n+# ttcgtcttttcagtcgtggctaaaaaaaaacattgccttcatatcaactgattatattttaccttcagaaatgtgcgctatggtcaatgtgatattag\n+# atgctaaaaatcaaagctttaaattgactactattgacggcattgatttgtataaatttcatgcaaaaattgacgaccaaatcgacaaagcgaatgta\n+# gctatgacacaaggtctaactggtaaacttatgtcagtgctagagtcgactttgtcaaaattagcacgatacgacgaaggtagcctaatcggctcgat\n+# tcttagttttacaaatgtatcgagctcgggaaaggatctcgggcaaggatatgtaaatttctttagaaataatatggatcaagtacgaggaaaaattg\n+# gcgacgatttatggaccctgaatttctttgagcagtggtactcgcagcagattaacatgctatgtaattggctttcggaacgtttggaccacgctctg\n+# cactacgctcaagtttcatctatttctcacattatcaagaaaatatattcagacttcgaattacaaggtgtattagaagataaattaaactctaaagc\n+# atatcaagcagtcgcacagcgaatggcgacagaggaagcgacatgtgctttgacaatgcctgatgttagcgaagatgaaccctgtgacgacattcgag\n+# aaggggaagaagaagatactggcgacgaatctacctctaacataccaaggggcttaccaaaaccaaaaattgctgccgctcaagctgctgctgttacc\n+# aacgttgttgccggccgtgtgggtaatttactcggcaaaggcattggcggccttagttcaaagttgggaagtggaagttggttttaa]\n+# protein sequence = [MIDPSSSEEEGEDDPIANVSSKGRLTHAPKGTNTVSILGGVSGPGVGSNMAISGSNGDLAGNQRQSNISSISNRNDAG\n+# NVAGVGGSSNKNEQIHGSRVDGGNLEVPNSCIPSGVSQETLNQSIGSSRANSLPRPLSPSPSLTSEKPDTGDPHAFLKGETQIMADEAFQNAVQSYHD\n+# VFLKSERVLKMVQSGASSQHDFREVFRNNIEKRVRSLPEIDGLSKETVLTSWMAKFDIILKGTGEEDSKRPSRMQQSLNSELILSKEQLYDMFQQILL\n+# VKKFEHQILYNALMLDSADEQAAAIRRELDGRMQRVGEMEKNRKLMPKFVLKEMESLYVEELKSSINLLMANLESLPVSKGNMDSKYGLQKLKRYNHR\n+# KLILRSHGSLSKLEGDSEDGSTQLTKLDVVLTFQLEVIVMEVKGLKSLAPNRIVYCTMEVENGEKLQTDQAEASKPMWDTQGDFTTTHPLPVVKVKLY\n+# TENPGMLALEDKELGKVILKPTPLSSKSPEWHRMVIPKNLPDQDIRIKIACRLDKPLNMKHCGYKEKKSEPSEMMQLDGYTVDYIEAASANLMFGIDL\n+# NGGRFFFNAVREGDSISFACDDENECSLWVMAMYRATGQSHKPTPPITQDKNSAMSKIQGARVAPDGSIFLWASFFVAAATRNSSSYHWFRVGGRLNP\n+# MVVSAAARMEWDMCAQSPLASTWRGIGWWSSSERGQPYDLVDVEVPKSGATHYHVSCRGEVNQPETVVRDGLMEAESTDGGVKDAFATELCVEVPEDK\n+# LHVVVWGWFSPGQVFVLDEYCARYGVRGCYRHLCYLSDLLDRAEKQHMIDPTLIHYSFAFCASHVHGNRPDGVGSITHEEKEKFSEIKERLRQLLEFQ\n+# ITNFRYCFPFGRPEGALKATLSLLERVLMKDIVTPVPPEEVRQMIKKSLETAALVNYTRLSNKAKIEGTFPFKGHVPGKSYRNFKIFPSTFLYTGNVP\n+# GKAYRKGPREIPSDIQDLRGEVIVPPPKKLEDLIHLAELCVDLLQQNEEHYGELRKHDKMDKIKMRKEDDDVPKGHNESDIDLTANTGLSSTSDLASA\n+# ASTNGSSFRYYNLRNGRFHQHLRDTFAPLVVRYVDLMESSIAQSIHKGFEKERWESKGNGCATSEDLFWKLDALQSFIRDLHWPDAEFRQHLEQRLKM\n+# MAVDMIEQCIQRTDSSFQSWLKKNIAFISTDYILPSEMCAMVNVILDAKNQSFKLTTIDGIDLYKFHAKIDDQIDKANVAMTQGLTGKLMSVLESTLS\n+# KLARYDEGSLIGSILSFTNVSSSGKDLGQGYVNFFRNNMDQVRGKIGDDLWTLNFFEQWYSQQINMLCNWLSERLDHALHYAQVSSISHIIKKIYSDF\n+# ELQGVLEDKLNSKAYQAVAQRMATEEATCALTMPDVSEDEPCDDIREGEEEDTGDESTSNIPRGLPKPKIAAAQAAAVTNVVAGRVGNLLGKGIGGLS\n+# SKLGSGSWF]\n+# end gene contig70.g117\n+###\n+# command line:\n+# augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /home/svc_galaxy/new/galaxy/database/files/000/dataset_98.dat --UTR=off --genemodel=complete --species=fly\n'

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/Dbia3/Dbia3.2bit

Binary file test-data/gff3/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track Augustus_Gene_Predictions.bb
+    longLabel Augustus Gene Predictions
+    shortLabel Augustus Gene P
+    bigDataUrl tracks/Augustus_Gene_Predictions.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb

Binary file test-data/gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/gff3/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,38 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1188.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gff3ToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpESpr1K.sorted.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpl9r8fF.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/916/dataset_1284_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gff3.Gff3 object at 0x1e8acd0>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/916/dataset_1284_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/gff3_multi_fasta_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/gff3_multi_fasta_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb">Multi-Fasta_GlimmerHMM_Gene_Predictions.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,2081 @@\n+##gff-version 3\n+##sequence-region contig1 1 45179\n+contig1\tGlimmerHMM\tmRNA\t641\t20329\t.\t-\t.\tID=contig1.path1.gene1;Name=contig1.path1.gene1\n+contig1\tGlimmerHMM\tCDS\t641\t5409\t.\t-\t2\tID=contig1.cds1.1;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t12541\t12968\t.\t-\t1\tID=contig1.cds1.2;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t14821\t14944\t.\t-\t2\tID=contig1.cds1.3;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t15123\t15424\t.\t-\t1\tID=contig1.cds1.4;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t17402\t17543\t.\t-\t2\tID=contig1.cds1.5;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t17886\t17986\t.\t-\t1\tID=contig1.cds1.6;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t20226\t20329\t.\t-\t0\tID=contig1.cds1.7;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=initial-exon\n+contig1\tGlimmerHMM\tmRNA\t22912\t26939\t.\t-\t.\tID=contig1.path1.gene2;Name=contig1.path1.gene2\n+contig1\tGlimmerHMM\tCDS\t22912\t23136\t.\t-\t0\tID=contig1.cds2.1;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t23431\t23705\t.\t-\t2\tID=contig1.cds2.2;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t26810\t26939\t.\t-\t0\tID=contig1.cds2.3;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=initial-exon\n+contig1\tGlimmerHMM\tmRNA\t29101\t41509\t.\t-\t.\tID=contig1.path1.gene3;Name=contig1.path1.gene3\n+contig1\tGlimmerHMM\tCDS\t29101\t29152\t.\t-\t1\tID=contig1.cds3.1;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=final-exon\n+contig1\tGlimmerHMM\tCDS\t31365\t33826\t.\t-\t0\tID=contig1.cds3.2;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t33880\t34044\t.\t-\t0\tID=contig1.cds3.3;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t34107\t34619\t.\t-\t0\tID=contig1.cds3.4;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t34674\t35311\t.\t-\t2\tID=contig1.cds3.5;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t35384\t35766\t.\t-\t1\tID=contig1.cds3.6;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon\n+contig1\tGlimmerHMM\tCDS\t41472\t41509\t.\t-\t0\tID=contig1.cds3.7;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=initial-exon\n+##sequence-region contig2 1 45017\n+contig2\tGlimmerHMM\tmRNA\t2231\t5162\t.\t-\t.\tID=contig2.path1.gene1;Name=contig2.path1.gene1\n+contig2\tGlimmerHMM\tCDS\t2231\t2376\t.\t-\t2\tID=contig2.cds1.1;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t2719\t2819\t.\t-\t1\tID=contig2.cds1.2;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t5059\t5162\t.\t-\t0\tID=contig2.cds1.3;Parent=contig2.path1.gene1;Name=contig2.path1.gene1;Note=initial-exon\n+contig2\tGlimmerHMM\tmRNA\t7745\t11772\t.\t-\t.\tID=contig2.path1.gene2;Name=contig2.path1.gene2\n+contig2\tGlimmerHMM\tCDS\t7745\t7969\t.\t-\t0\tID=contig2.cds2.1;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t8264\t8538\t.\t-\t2\tID=contig2.cds2.2;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t11643\t11772\t.\t-\t0\tID=contig2.cds2.3;Parent=contig2.path1.gene2;Name=contig2.path1.gene2;Note=initial-exon\n+contig2\tGlimmerHMM\tmRNA\t13934\t36373\t.\t-\t.\tID=contig2.path1.gene3;Name=contig2.path1.gene3\n+contig2\tGlimmerHMM\tCDS\t13934\t13985\t.\t-\t1\tID=contig2.cds3.1;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;Note=final-exon\n+contig2\tGlimmerHMM\tCDS\t16198\t18659\t.\t-\t0\tID=contig2.cds3.2;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;Note=internal-exon\n+contig2\tGlimmerHMM\tCDS\t18713\t18877\t.\t-\t0\tID=contig2.cds3.3;Parent=contig2.path1.gene3;Name=contig2.path1.gene3;N'..b'9\t12828\t.\t+\t1\tID=contig70.cds1.10;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t12886\t13092\t.\t+\t2\tID=contig70.cds1.11;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t15494\t15832\t.\t+\t2\tID=contig70.cds1.12;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t15998\t16096\t.\t+\t2\tID=contig70.cds1.13;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t16376\t16723\t.\t+\t2\tID=contig70.cds1.14;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t16861\t17074\t.\t+\t2\tID=contig70.cds1.15;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t17114\t17366\t.\t+\t1\tID=contig70.cds1.16;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t21277\t21354\t.\t+\t0\tID=contig70.cds1.17;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t21531\t21822\t.\t+\t0\tID=contig70.cds1.18;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t22845\t22924\t.\t+\t2\tID=contig70.cds1.19;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t24039\t24226\t.\t+\t0\tID=contig70.cds1.20;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t24288\t24577\t.\t+\t1\tID=contig70.cds1.21;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t27274\t27411\t.\t+\t2\tID=contig70.cds1.22;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t28524\t28636\t.\t+\t2\tID=contig70.cds1.23;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t31963\t32034\t.\t+\t0\tID=contig70.cds1.24;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t33015\t33225\t.\t+\t0\tID=contig70.cds1.25;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t36266\t36324\t.\t+\t2\tID=contig70.cds1.26;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t36995\t37151\t.\t+\t0\tID=contig70.cds1.27;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t38419\t38560\t.\t+\t2\tID=contig70.cds1.28;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t38856\t39023\t.\t+\t1\tID=contig70.cds1.29;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t45726\t46035\t.\t+\t1\tID=contig70.cds1.30;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t46098\t46478\t.\t+\t0\tID=contig70.cds1.31;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t46932\t47068\t.\t+\t0\tID=contig70.cds1.32;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t47124\t47317\t.\t+\t1\tID=contig70.cds1.33;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t50861\t51057\t.\t+\t2\tID=contig70.cds1.34;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t51487\t51513\t.\t+\t0\tID=contig70.cds1.35;Parent=contig70.path1.gene1;Name=contig70.path1.gene1;Note=final-exon\n+contig70\tGlimmerHMM\tmRNA\t54155\t54504\t.\t+\t.\tID=contig70.path1.gene2;Name=contig70.path1.gene2\n+contig70\tGlimmerHMM\tCDS\t54155\t54191\t.\t+\t0\tID=contig70.cds2.1;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=initial-exon\n+contig70\tGlimmerHMM\tCDS\t54315\t54370\t.\t+\t2\tID=contig70.cds2.2;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=internal-exon\n+contig70\tGlimmerHMM\tCDS\t54472\t54504\t.\t+\t0\tID=contig70.cds2.3;Parent=contig70.path1.gene2;Name=contig70.path1.gene2;Note=final-exon\n'

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/Dbia3/Dbia3.2bit

Binary file test-data/gff3_multi_fasta/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+    longLabel Multi-Fasta GlimmerHMM Gene Predictions
+    shortLabel Multi-Fasta Gli
+    bigDataUrl tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb

Binary file test-data/gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/gff3_multi_fasta/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gff3_multi_fasta/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/glimmerHMM_output.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/glimmerHMM_output.gff3 Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,22 @@
+##gff-version 3
+##sequence-region contig1 1 45179
+contig1 GlimmerHMM mRNA 641 20329 . - . ID=contig1.path1.gene1;Name=contig1.path1.gene1
+contig1 GlimmerHMM CDS 641 5409 . - 2 ID=contig1.cds1.1;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=final-exon
+contig1 GlimmerHMM CDS 12541 12968 . - 1 ID=contig1.cds1.2;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon
+contig1 GlimmerHMM CDS 14821 14944 . - 2 ID=contig1.cds1.3;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon
+contig1 GlimmerHMM CDS 15123 15424 . - 1 ID=contig1.cds1.4;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon
+contig1 GlimmerHMM CDS 17402 17543 . - 2 ID=contig1.cds1.5;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon
+contig1 GlimmerHMM CDS 17886 17986 . - 1 ID=contig1.cds1.6;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=internal-exon
+contig1 GlimmerHMM CDS 20226 20329 . - 0 ID=contig1.cds1.7;Parent=contig1.path1.gene1;Name=contig1.path1.gene1;Note=initial-exon
+contig1 GlimmerHMM mRNA 22912 26939 . - . ID=contig1.path1.gene2;Name=contig1.path1.gene2
+contig1 GlimmerHMM CDS 22912 23136 . - 0 ID=contig1.cds2.1;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=final-exon
+contig1 GlimmerHMM CDS 23431 23705 . - 2 ID=contig1.cds2.2;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=internal-exon
+contig1 GlimmerHMM CDS 26810 26939 . - 0 ID=contig1.cds2.3;Parent=contig1.path1.gene2;Name=contig1.path1.gene2;Note=initial-exon
+contig1 GlimmerHMM mRNA 29101 41509 . - . ID=contig1.path1.gene3;Name=contig1.path1.gene3
+contig1 GlimmerHMM CDS 29101 29152 . - 1 ID=contig1.cds3.1;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=final-exon
+contig1 GlimmerHMM CDS 31365 33826 . - 0 ID=contig1.cds3.2;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon
+contig1 GlimmerHMM CDS 33880 34044 . - 0 ID=contig1.cds3.3;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon
+contig1 GlimmerHMM CDS 34107 34619 . - 0 ID=contig1.cds3.4;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon
+contig1 GlimmerHMM CDS 34674 35311 . - 2 ID=contig1.cds3.5;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon
+contig1 GlimmerHMM CDS 35384 35766 . - 1 ID=contig1.cds3.6;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=internal-exon
+contig1 GlimmerHMM CDS 41472 41509 . - 0 ID=contig1.cds3.7;Parent=contig1.path1.gene3;Name=contig1.path1.gene3;Note=initial-exon

diff -r 000000000000 -r f493979f1408 test-data/gtf/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,38 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp4nx0OH.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpaKvcsw.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/910/dataset_1278_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x2b0dd10>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/910/dataset_1278_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/gtf/gtf_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/gtf_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/gtf/inputs/StringTie_Assembled_Transcripts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/inputs/StringTie_Assembled_Transcripts Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+# stringtie /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat -o /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat -p 1
+# StringTie version 1.2.3
+contig16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "866155.937500";
+contig16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892";
+contig16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081";
+contig16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477";
+contig16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721";
+contig16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867";
+contig16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496";
+contig16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709";
+contig16 StringTie exon 17406 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873";

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/Dbia3/Dbia3.2bit

Binary file test-data/gtf/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track StringTie_Assembled_Transcripts.bb
+    longLabel StringTie Assembled Transcripts
+    shortLabel StringTie Assem
+    bigDataUrl tracks/StringTie_Assembled_Transcripts.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/gtf/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/gtf_gff_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/gtf_gff_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,73 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb">Augustus_Gene_Predictions.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/Dbia3/Dbia3.2bit

Binary file test-data/gtf_gff/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb

Binary file test-data/gtf_gff/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/gtf_gff/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/gtf_gff/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf_gff/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/only_genome/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_genome/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,16 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: []
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/only_genome/myHub/Dbia3/Dbia3.2bit

Binary file test-data/only_genome/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/only_genome/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_genome/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/only_genome/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_genome/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/only_genome/only_genome.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/only_genome/only_genome.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,54 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/psl/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,36 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1033.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'blastXmlToPsl', u'track_color': u'#00b050', u'group_name': u'Default group'}
+DEBUG:root:Calling pslToBigPsl:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Hello
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp0NXyEzpsl
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpG8McOt.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/967/dataset_1334_files/myHub/Dbia3/tracks/blastXmlToPsl.bb
+DEBUG:root:typeOption: bed12+12
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/testtoolshed.g2.bx.psu.edu/repos/remimarenco/hubarchivecreator/b40c942bbcc0/hubarchivecreator/bigPsl.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Psl.Psl object at 0x155bb90>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/967/dataset_1334_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track blastXmlToPsl.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/psl/inputs/blastXmlToPsl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/inputs/blastXmlToPsl Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+1458 762 183 0 7 60 10 57 +- ci-PA 4191 1725 4188 contig1 45179 31366 33826 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1725,1890,2391,2448,2472,2622,2745,2889,3006,3114,3324,3369,3438,3528,3720,3894,3930,4062, 11353,11524,12019,12067,12097,12250,12379,12529,12649,12763,12967,13018,13099,13183,13369,13546,13573,13687,
+987 300 231 0 1 3 5 141 +- ci-PA 4191 39 1560 contig1 45179 34106 35765 7 174,45,63,84,432,210,510, 39,213,258,321,405,840,1050, 9414,9594,9642,9711,9867,10299,10563,
+162 3 0 0 0 0 0 0 +- ci-PA 4191 1560 1725 contig1 45179 33879 34044 1 165, 1560, 11135,
+39 0 0 0 0 0 0 0 +- ci-PA 4191 0 39 contig1 45179 41470 41509 1 39, 0, 3670,
+1050 336 231 0 1 3 6 270 +- ci-PC 1716 39 1659 contig1 45179 33878 35765 8 171,48,63,84,432,210,510,99, 39,210,258,321,405,840,1050,1560, 9414,9591,9642,9711,9867,10299,10563,11202,
+111 138 0 0 0 0 4 39 +- ci-PC 1716 1467 1716 contig1 45179 33768 34056 5 45,54,51,36,63, 1467,1512,1566,1617,1653, 11123,11177,11237,11300,11348,
+39 0 0 0 0 0 0 0 +- ci-PC 1716 0 39 contig1 45179 41470 41509 1 39, 0, 3670,
+1458 762 183 0 7 60 10 57 +- ci-PB 3837 1371 3834 contig1 45179 31366 33826 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1371,1536,2037,2094,2118,2268,2391,2535,2652,2760,2970,3015,3084,3174,3366,3540,3576,3708, 11353,11524,12019,12067,12097,12250,12379,12529,12649,12763,12967,13018,13099,13183,13369,13546,13573,13687,
+834 264 105 0 1 3 2 126 +- ci-PB 3837 0 1206 contig1 45179 34106 35435 4 51,432,210,510, 0,51,486,696, 9744,9867,10299,10563,
+162 3 0 0 0 0 0 0 +- ci-PB 3837 1206 1371 contig1 45179 33879 34044 1 165, 1206, 11135,

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/Dbia3/Dbia3.2bit

Binary file test-data/psl/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+    track blastXmlToPsl.bb
+    longLabel blastXmlToPsl
+    shortLabel blastXmlToPsl
+    bigDataUrl tracks/blastXmlToPsl.bb
+    type bigPsl
+    visibility dense
+    thickDrawItem off
+    priority 10
+    color 0,176,80
+    group default_group
+

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/Dbia3/tracks/blastXmlToPsl.bb

Binary file test-data/psl/myHub/Dbia3/tracks/blastXmlToPsl.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+genome Dbia3
+trackDb Dbia3/trackDb.txt
+groups Dbia3/groups.txt
+description Dbia3
+twoBitPath Dbia3/Dbia3.2bit
+organism Dbia3
+defaultPos contig1
+orderKey 4500
+scientificName Dbia3
+htmlPath Dbia3/description.html

diff -r 000000000000 -r f493979f1408 test-data/psl/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/psl/psl_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/psl/psl_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/blastXmlToPsl.bb">blastXmlToPsl.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,38 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1329.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmptjLL_6.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmp5N24Cj.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/964/dataset_1331_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Gtf.Gtf object at 0x179fd10>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/964/dataset_1331_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/inputs/stringtie_assembled_transcripts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/inputs/stringtie_assembled_transcripts Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,11 @@
+# stringtie /home/svc_galaxy/new/galaxy/database/files/001/dataset_1102.dat -o /home/svc_galaxy/new/galaxy/database/files/001/dataset_1103.dat -p 1
+# StringTie version 1.1.0
+contig16 StringTie transcript 1751 17824 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "14.618678"; FPKM "322160.531250"; TPM "880020.875000";
+contig16 StringTie exon 1751 1897 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "6.787892";
+contig16 StringTie exon 11285 11463 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "19.860081";
+contig16 StringTie exon 11518 11705 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "23.926477";
+contig16 StringTie exon 11759 11858 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "17.452721";
+contig16 StringTie exon 11922 11975 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "11.461867";
+contig16 StringTie exon 12601 12811 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "11.876496";
+contig16 StringTie exon 17222 17337 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "15.915709";
+contig16 StringTie exon 17406 45020 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "8"; cov "11.738873";

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/Dbia3.2bit

Binary file test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/tblastN/dbia3.xml.bb

Binary file test-data/tblastN/dbia3.xml.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/tblastN/dbia3.xml.sorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/dbia3.xml.sorted.bed Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0,
+contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0,
+contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278,
+contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig1 41470 41509 ci-PA 1000 - 41470 41509 0 1 39, 0,
+contig1 41470 41509 ci-PC 1000 - 41470 41509 0 1 39, 0,

diff -r 000000000000 -r f493979f1408 test-data/tblastN/dbia3.xml.unbb.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/dbia3.xml.unbb.bed Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/tblastN/dbia3.xml.unsorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/dbia3.xml.unsorted.bed Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0,
+contig1 41470 41509 ci-PA 1000 - 41470 41509 0 1 39, 0,
+contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig1 41470 41509 ci-PC 1000 - 41470 41509 0 1 39, 0,
+contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278,
+contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0,

diff -r 000000000000 -r f493979f1408 test-data/tblastN/hubaInputs/tblastn_Dbia3_ci.xml.sorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/hubaInputs/tblastn_Dbia3_ci.xml.sorted.bed Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,50 @@
+contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0,
+contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0,
+contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278,
+contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig2 16199 18659 ci-PA 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 16199 18659 ci-PB 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 18601 18889 ci-PC 0 - 18601 18889 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig2 18711 20598 ci-PC 584 - 18711 20598 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig2 18712 18877 ci-PA 964 - 18712 18877 0 1 165, 0,
+contig2 18712 18877 ci-PB 964 - 18712 18877 0 1 165, 0,
+contig2 18939 20268 ci-PB 560 - 18939 20268 0 4 510,210,432,51, 0,564,774,1278,
+contig2 18939 20598 ci-PA 604 - 18939 20598 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig23 23849 24035 ci-PA 0 - 23849 24035 0 3 51,21,96, 0,51,90,
+contig23 23849 24035 ci-PB 0 - 23849 24035 0 3 51,21,96, 0,51,90,
+contig23 32405 32564 ci-PA 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32564 ci-PB 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32573 ci-PA 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig23 32405 32573 ci-PB 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig23 32471 32564 ci-PC 0 - 32471 32564 0 1 93, 0,
+contig24 3846 4032 ci-PA 0 - 3846 4032 0 3 51,21,96, 0,51,90,
+contig24 3846 4032 ci-PB 0 - 3846 4032 0 3 51,21,96, 0,51,90,
+contig24 12402 12561 ci-PA 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12561 ci-PB 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12570 ci-PA 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig24 12402 12570 ci-PB 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig24 12468 12561 ci-PC 0 - 12468 12561 0 1 93, 0,
+contig66 33180 33312 ci-PA 0 - 33180 33312 0 1 132, 0,
+contig66 33180 33312 ci-PB 0 - 33180 33312 0 1 132, 0,
+contig66 33204 33303 ci-PA 0 - 33204 33303 0 1 99, 0,
+contig66 33204 33303 ci-PB 0 - 33204 33303 0 1 99, 0,
+contig66 35474 35663 ci-PA 0 - 35474 35663 0 1 189, 0,
+contig66 35474 35663 ci-PB 0 - 35474 35663 0 1 189, 0,
+contig66 35516 35762 ci-PA 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35516 35762 ci-PB 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35534 35756 ci-PA 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig66 35534 35756 ci-PB 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig67 18177 18309 ci-PA 0 - 18177 18309 0 1 132, 0,
+contig67 18177 18309 ci-PB 0 - 18177 18309 0 1 132, 0,
+contig67 18201 18300 ci-PA 0 - 18201 18300 0 1 99, 0,
+contig67 18201 18300 ci-PB 0 - 18201 18300 0 1 99, 0,
+contig67 20471 20660 ci-PA 0 - 20471 20660 0 1 189, 0,
+contig67 20471 20660 ci-PB 0 - 20471 20660 0 1 189, 0,
+contig67 20513 20759 ci-PA 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20513 20759 ci-PB 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20531 20753 ci-PA 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,
+contig67 20531 20753 ci-PB 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,

diff -r 000000000000 -r f493979f1408 test-data/tblastN/readme/README.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/readme/README.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,36 @@
+<h1 id="conversion-of-ncbi-blast-tblastn-results-to-psl-format">Conversion of NCBI BLAST+ tblastn results to PSL format</h1>
+<p>Wilson Leung <script type="text/javascript">
+
+</script><noscript>wleung at wustl dot edu</noscript></p>
+<p>Last Update: 04/24/2016</p>
+<h2 id="version-information">Version information</h2>
+<ul>
+<li>Kent source tree: v324</li>
+<li>NCBI BLAST+: BLAST 2.2.30+</li>
+</ul>
+<h2 id="data-sources">Data sources</h2>
+<p>For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the <em>D. melanogaster</em> <em>ci</em> gene in contig1. The protein sequences are available through <a href="http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation">FlyBase</a>.</p>
+<ul>
+<li>Dbia3.fa = contig1 sequence in the Dbia3 asssembly</li>
+<li>ci.pep = Protein sequences for the three isoforms of the <em>ci</em> gene in <em>D. melanogaster</em></li>
+</ul>
+<h2 id="conversion-protocol">Conversion protocol</h2>
+<ol style="list-style-type: decimal">
+<li><p>Create BLAST database for the assembly</p>
+<pre><code>makeblastdb -in Dbia3.fa -dbtype nucl</code></pre></li>
+<li><p>Perform tblastn search and output results in XML format</p>
+<pre><code>tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2</code></pre></li>
+<li><p>Convert results into PSL format</p>
+<pre><code>blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl</code></pre></li>
+<li><p>Convert PSL output into BED format</p>
+<pre><code>pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed</code></pre></li>
+</ol>
+<h2 id="output-files">Output files</h2>
+<ul>
+<li>tblastn_Dbia3_ci.xml = tblastn results in XML format</li>
+<li>tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format</li>
+<li>tblastn_Dbia3_ci.xml.bed = tblastn results in BED format</li>
+</ul>

diff -r 000000000000 -r f493979f1408 test-data/tblastN/readme/README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/readme/README.md Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,48 @@
+Conversion of NCBI BLAST+ tblastn results to PSL format
+=======================================================
+Wilson Leung <wleung@wustl.edu>
+
+Last Update: 04/24/2016
+
+
+Version information
+-------------------
+* Kent source tree: v324
+* NCBI BLAST+: BLAST 2.2.30+
+
+Data sources
+-------------------
+For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the *D. melanogaster* *ci* gene in contig1. The protein sequences are available through [FlyBase](http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation).
+
+* Dbia3.fa = contig1 sequence in the Dbia3 asssembly
+* ci.pep = Protein sequences for the three isoforms of the *ci* gene in *D. melanogaster*
+
+Conversion protocol
+-----------------------
+1. Create BLAST database for the assembly
+```
+makeblastdb -in Dbia3.fa -dbtype nucl
+```
+
+2. Perform tblastn search and output results in XML format
+```
+tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2
+```
+
+3. Convert results into PSL format
+```
+blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl
+```
+
+4. Convert PSL output into BED format
+```
+pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed
+```
+
+Output files
+-----------------------
+* tblastn_Dbia3_ci.xml = tblastn results in XML format
+* tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format
+* tblastn_Dbia3_ci.xml.bed = tblastn results in BED format
+
+

diff -r 000000000000 -r f493979f1408 test-data/tblastN/workflowInputs/ci.pep
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/workflowInputs/ci.pep Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,45 @@
+>ci-PA FBpp0088245
+MDAYALPTYFPLAYSELQFLASRRAAAVAAAATVLPGSPCINQHHPTDVSSSVTVPSIIPTGGTSDSIKTSIQPQICNEN
+TLLGNAGHQHNHQPQHVHNINVTGQPHDFHPAYRIPGYMEQLYSLQRTNSASSFHDPYVNCASAFHLAGLGLGSADFLGS
+RGLSSLGELHNAAVAAAAAGSLASTDFHFSVDGNRRLGSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLA
+TIMNGSRGSSAASGSYGHISATALNPMSHVHSTRLQQIQAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVH
+PNLSDSHIQITTSPTVTKDVSQVPAAAFSLKNLDDAREKKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVN
+NITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADTTDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTN
+KKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCTFEGCFKAYSRLENLKTHLRSHTGEKPYTCEYPGCSKAFSN
+ASDRAKHQNRTHSNEKPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLQQNNSRHNLQEHNID
+SSPCSEDSHLGKMLGTSSPSIKSESDISSSNHHLVNGVRASDSLLTYSPDDLAENLNLDDGWNCDDDVDVADLPIVLRAM
+VNIGNGNASASTIGGSVLARQRFRGRLQTKGINSSTIMLCNIPESNRTFGISELNQRITELKMEPGTDAEIKIPKLPNTT
+IGGYTEDPLQNQTSFRNTVSNKQGTVSGSIQGQFRRDSQNSTASTYYGSMQSRRSSQSSQVSSIPTMRPNPSCNSTASFY
+DPISPGCSRRSSQMSNGANCNSFTSTSGLPVLNKESNKSLNACINKPNIGVQGVGIYNSSLPPPPSSHLIATNLKRLQRK
+DSEYHNFTSGRFSVPSYMHSLHIKNNKPVGENEFDKAIASNARRQTDPVPNINLDPLTNISRFSTTPHSFDINVGKTNNI
+ASSINKDNLRKDLFTVSIKADMAMTSDQHPNERINLDEVEELILPDEMLQYLNLVKDDTNHLEKEHQAVPVGSNVSETIA
+SNHYREQSNIYYTNKQILTPPSNVDIQPNTTKFTVQDKFAMTAVGGSFSQRELSTLAVPNEHGHAKCESFHHQSQKYMNT
+DIGSKQQSALPSAHQRQTEKSNYNQIIDSSMTSLPELNVDSIYPRNETENIFKVHGDHDNEIQCGIISQSQMSPSTNLNN
+DGQFSTVNMQPITTSKLFPPEPQKIVCDTQASNTSVMHLDTYQRTLEYVQSCQNWMETNNTSTNQIQSLPGMPVNNTLFP
+DVSSSTHPYHGTNMVINDMTTSLTSLLEENRYLQMMQ
+>ci-PC FBpp0300417
+MDAYALPTYFPLAYSELQFLASRRAAAVAAAATVLPGSPCINQHHPTDVSSSVTVPSIIPTGGTSDSIKTSIQPQICNEN
+TLLGNAGHQHNHQPQHVHNINVTGQPHDFHPAYRIPGYMEQLYSLQRTNSASSFHDPYVNCASAFHLAGLGLGSADFLGS
+RGLSSLGELHNAAVAAAAAGSLASTDFHFSVDGNRRLGSPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLA
+TIMNGSRGSSAASGSYGHISATALNPMSHVHSTRLQQIQAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVH
+PNLSDSHIQITTSPTVTKDVSQVPAAAFSLKNLDDAREKKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVN
+NITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADTTDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTN
+KKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCTEKNHTLASIRDVAKPLVMLVIAQSIKIEHTVMRNRTFVKH
+LDAQNVTPTRAL
+>ci-PB FBpp0297298
+MEQLYSLQRTNSASSFHDPYVNCASAFHLAGLGLGSADFLGSRGLSSLGELHNAAVAAAAAGSLASTDFHFSVDGNRRLG
+SPRPPGGSIRASISRKRALSSSPYSDSFDINSMIRFSPNSLATIMNGSRGSSAASGSYGHISATALNPMSHVHSTRLQQI
+QAHLLRASAGLLNPMTPQQVAASGFSIGHMPTSASLRVNDVHPNLSDSHIQITTSPTVTKDVSQVPAAAFSLKNLDDARE
+KKGPFKDVVPEQPSSTSGGVAQVEADSASSQLSDRCYNNVVNNITGIPGDVKVNSRLDEYINCGSISIPSNEYDCANADT
+TDIKDEPGDFIETNCHWRSCRIEFITQDELVKHINNDHIQTNKKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHK
+CTFEGCFKAYSRLENLKTHLRSHTGEKPYTCEYPGCSKAFSNASDRAKHQNRTHSNEKPYICKAPGCTKRYTDPSSLRKH
+VKTVHGAEFYANKKHKGLPLNDANSRLQQNNSRHNLQEHNIDSSPCSEDSHLGKMLGTSSPSIKSESDISSSNHHLVNGV
+RASDSLLTYSPDDLAENLNLDDGWNCDDDVDVADLPIVLRAMVNIGNGNASASTIGGSVLARQRFRGRLQTKGINSSTIM
+LCNIPESNRTFGISELNQRITELKMEPGTDAEIKIPKLPNTTIGGYTEDPLQNQTSFRNTVSNKQGTVSGSIQGQFRRDS
+QNSTASTYYGSMQSRRSSQSSQVSSIPTMRPNPSCNSTASFYDPISPGCSRRSSQMSNGANCNSFTSTSGLPVLNKESNK
+SLNACINKPNIGVQGVGIYNSSLPPPPSSHLIATNLKRLQRKDSEYHNFTSGRFSVPSYMHSLHIKNNKPVGENEFDKAI
+ASNARRQTDPVPNINLDPLTNISRFSTTPHSFDINVGKTNNIASSINKDNLRKDLFTVSIKADMAMTSDQHPNERINLDE
+VEELILPDEMLQYLNLVKDDTNHLEKEHQAVPVGSNVSETIASNHYREQSNIYYTNKQILTPPSNVDIQPNTTKFTVQDK
+FAMTAVGGSFSQRELSTLAVPNEHGHAKCESFHHQSQKYMNTDIGSKQQSALPSAHQRQTEKSNYNQIIDSSMTSLPELN
+VDSIYPRNETENIFKVHGDHDNEIQCGIISQSQMSPSTNLNNDGQFSTVNMQPITTSKLFPPEPQKIVCDTQASNTSVMH
+LDTYQRTLEYVQSCQNWMETNNTSTNQIQSLPGMPVNNTLFPDVSSSTHPYHGTNMVINDMTTSLTSLLEENRYLQMMQ

diff -r 000000000000 -r f493979f1408 test-data/tblastN/workflowInputs/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/workflowInputs/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,1174 @@\n+<?xml version="1.0"?>\n+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n+<BlastOutput>\n+ <BlastOutput_program>tblastn</BlastOutput_program>\n+ <BlastOutput_version>TBLASTN 2.3.0+</BlastOutput_version>\n+ <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n+ <BlastOutput_db>dbia3.fasta</BlastOutput_db>\n+ <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n+ <BlastOutput_query-def>ci-PA FBpp0088245</BlastOutput_query-def>\n+ <BlastOutput_query-len>1397</BlastOutput_query-len>\n+ <BlastOutput_param>\n+ <Parameters>\n+ <Parameters_matrix>BLOSUM62</Parameters_matrix>\n+ <Parameters_expect>0.01</Parameters_expect>\n+ <Parameters_gap-open>11</Parameters_gap-open>\n+ <Parameters_gap-extend>1</Parameters_gap-extend>\n+ <Parameters_filter>L;</Parameters_filter>\n+ </Parameters>\n+ </BlastOutput_param>\n+<BlastOutput_iterations>\n+<Iteration>\n+ <Iteration_iter-num>1</Iteration_iter-num>\n+ <Iteration_query-ID>Query_1</Iteration_query-ID>\n+ <Iteration_query-def>ci-PA FBpp0088245</Iteration_query-def>\n+ <Iteration_query-len>1397</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gnl|BL_ORD_ID|1</Hit_id>\n+ <Hit_def>contig2</Hit_def>\n+ <Hit_accession>1</Hit_accession>\n+ <Hit_len>45017</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>852.818</Hsp_bit-score>\n+ <Hsp_score>2202</Hsp_score>\n+ <Hsp_evalue>0</Hsp_evalue>\n+ <Hsp_query-from>576</Hsp_query-from>\n+ <Hsp_query-to>1396</Hsp_query-to>\n+ <Hsp_hit-from>16200</Hsp_hit-from>\n+ <Hsp_hit-to>18659</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>-1</Hsp_hit-frame>\n+ <Hsp_identity>540</Hsp_identity>\n+ <Hsp_positive>627</Hsp_positive>\n+ <Hsp_gaps>39</Hsp_gaps>\n+ <Hsp_align-len>840</Hsp_align-len>\n+ <Hsp_qseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLQQNNS--RHNLQEHNIDSSPCSEDSHLGKMLGTXXXXXXXXXXXXXXNHHLVNGVRASDSLLTYSPDDLAEXXXXXXXXXXXXXXXXXXXXXXXRAMVNIGNGNASASTIGGSVLARQRFRGRLQTKGINSSTIMLCNIPESNRTFGISELNQRITELKMEPGTDAEIKIPKLPNTTIGGYTEDPLQNQTSFRNTVSNKQG--TVSGSIQGQFRRDSQNSTASTYYGXXXXXXXXXXXXXXXIPTMRPNPSCN-STASFYDPISPGCSRRSSQMSNGANCNSFTSTSGLPVLNKE--SNKSLNACINKPNIGVQGVGIYNXXXXXXXXXHLIATNLKRLQRKDSE--YHNFTSGRFSVPSYMHSLHIKNNKPVGENEFDKAIASNA-RRQTDPVPNINLDPLTNISRFSTTPHSFDINVGKTN--NIASSINKDNLRKDLFTVSIKADMAMTSDQHPNERINLDEVEELILPDEMLQYLNLVKDDTNHLEKEHQAVPVGSNVSETIASNH--YREQSNIYYTNKQILTPPSNVDI----QPNTTKFTVQDKFAMTAVGGSFSQRELSTLAVPNEHGHAKCESFHHQSQKYMNTDIGSKQQSALPSAHQRQTEKSNYNQIIDSSMTSLPELNVDSIYPRNETENIFKVHGDHDNEIQCGIISQSQMSPSTNLNNDGQFSTVNMQPITTSKLF-PPEPQKIVCDTQASNTSVMHLDTYQRTLEYVQSCQNWMETNNTSTNQIQSLPGMPVNNTLFPDVSSSTHPYHGTNMVINDMTTSLTSLLEENRYLQMM</Hsp_qseq>\n+ <Hsp_hseq>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRLHRDSGQGRHNLQEHNIDSSPCSEELQVGKLIGMSSPSIKSESDESSPHHQLLSGVRASDCFLTYSQDGAAEHITLDDGWDCDDDVDVADLPIVLRAMVNVGSGNSMAPTIGGGVVARQRFRSRLQTKGINSSMVMLGNIPESNRTIGISELNQRITELKMEPGTACDITVPL--NTGLERISEDLSQNQS---NITLNKQSFFTASGSLQGHFRRDSQNSTASTYYGSMQSRRSSQSSQVSSISTMRPGPSYNTTTASLYDPISPGCSRRSSQMSNVVNSYALTSTSGLTAINKDLNANSSPNASINKPGLGGQYFGFYNNSLPPPPSSHLIATNLKHLQDTDSRSCYHNTTGGRFSIPNCTPSLHLDYNGPAGEQEIDKEIPNNILRRQSEPMPNISLDTLTNVSPLSGPLQNLQFPIGKARNVNITSSSNENTLRKGPCHATMKTEMTMTSEQHPNERINLDEVEELILPDEMLQYLNLVKDDQNYMEKDD--VAIRSTVPKTIKSNENLLLSKSNLNPIKKQIILPTSNFDVSINLQPNTSNLQTQEEHTMTTIGGLPSQREQN--IVPHQHEKTKCRSFPQEIDKTINIDIGFKEQPYPSSAYQPQITKSNQNEIIDSSMTSLPELN--PIFTKINSENVSKLHRDQNSEIQCGIVSQSQMSPSININNDGETSTLKNLPLTYSKFSGQPNTQTTVG---GSNTSSMVSDTYQRTLEYVQSCQNWVDTNNSSGDQIQS------NNTLWSDVSSSTHPYAGTNLVINDMTTSLTSLLEENRYLHMM</Hsp_hseq>\n+ <Hsp_midline>KPYICKAPGCTKRYTDPSSLRKHVKTVHGAEFYANKKHKGLPLNDANSRL +++ R'..b' <Hsp_midline>H +K C +GC K + ++ HL +H G + + C C KAF +S +HQ H+ EKP+ C GC KR++ +LR</Hsp_midline>\n+ </Hsp>\n+ <Hsp>\n+ <Hsp_num>2</Hsp_num>\n+ <Hsp_bit-score>47.3654</Hsp_bit-score>\n+ <Hsp_score>111</Hsp_score>\n+ <Hsp_evalue>6.65795e-06</Hsp_evalue>\n+ <Hsp_query-from>362</Hsp_query-from>\n+ <Hsp_query-to>441</Hsp_query-to>\n+ <Hsp_hit-from>35535</Hsp_hit-from>\n+ <Hsp_hit-to>35756</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>-1</Hsp_hit-frame>\n+ <Hsp_identity>29</Hsp_identity>\n+ <Hsp_positive>37</Hsp_positive>\n+ <Hsp_gaps>6</Hsp_gaps>\n+ <Hsp_align-len>80</Hsp_align-len>\n+ <Hsp_qseq>NKKAFVCRWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCTFEGCFKAYSRLENLKTHLRSHTGEKPYTCEYPGCSKAFS</Hsp_qseq>\n+ <Hsp_hseq>NDKKIACPHKGC---HKNFRDSSAMRKHLHTH-GPRVHVCA--ECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFS</Hsp_hseq>\n+ <Hsp_midline>N K C + C K F+ + H+ H G + H C C KA+ LK H HTGEKP+ C + GC K FS</Hsp_midline>\n+ </Hsp>\n+ <Hsp>\n+ <Hsp_num>3</Hsp_num>\n+ <Hsp_bit-score>41.5874</Hsp_bit-score>\n+ <Hsp_score>96</Hsp_score>\n+ <Hsp_evalue>0.000398301</Hsp_evalue>\n+ <Hsp_query-from>384</Hsp_query-from>\n+ <Hsp_query-to>427</Hsp_query-to>\n+ <Hsp_hit-from>33181</Hsp_hit-from>\n+ <Hsp_hit-to>33312</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>-3</Hsp_hit-frame>\n+ <Hsp_identity>16</Hsp_identity>\n+ <Hsp_positive>28</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>44</Hsp_align-len>\n+ <Hsp_qseq>YMLVVHMRRHTGEKPHKCTFEGCFKAYSRLENLKTHLRSHTGEK</Hsp_qseq>\n+ <Hsp_hseq>FIYRTHVRIHTGDRPFVCPFDACNKKFAQSTNLKSHILTHAKAK</Hsp_hseq>\n+ <Hsp_midline>++ H+R HTG++P C F+ C K +++ NLK+H+ +H K</Hsp_midline>\n+ </Hsp>\n+ <Hsp>\n+ <Hsp_num>4</Hsp_num>\n+ <Hsp_bit-score>40.817</Hsp_bit-score>\n+ <Hsp_score>94</Hsp_score>\n+ <Hsp_evalue>0.000632218</Hsp_evalue>\n+ <Hsp_query-from>369</Hsp_query-from>\n+ <Hsp_query-to>431</Hsp_query-to>\n+ <Hsp_hit-from>35475</Hsp_hit-from>\n+ <Hsp_hit-to>35663</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>-1</Hsp_hit-frame>\n+ <Hsp_identity>23</Hsp_identity>\n+ <Hsp_positive>28</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>63</Hsp_align-len>\n+ <Hsp_qseq>RWEDCTRGEKPFKAQYMLVVHMRRHTGEKPHKCTFEGCFKAYSRLENLKTHLRSHTGEKPYTC</Hsp_qseq>\n+ <Hsp_hseq>RVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRYSTKKFWFSYKFVC</Hsp_hseq>\n+ <Hsp_midline>R C K F L H HTGEKP +CTFEGC K +S NL+ + + C</Hsp_midline>\n+ </Hsp>\n+ <Hsp>\n+ <Hsp_num>5</Hsp_num>\n+ <Hsp_bit-score>37.7354</Hsp_bit-score>\n+ <Hsp_score>86</Hsp_score>\n+ <Hsp_evalue>0.00636923</Hsp_evalue>\n+ <Hsp_query-from>417</Hsp_query-from>\n+ <Hsp_query-to>449</Hsp_query-to>\n+ <Hsp_hit-from>33205</Hsp_hit-from>\n+ <Hsp_hit-to>33303</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>-3</Hsp_hit-frame>\n+ <Hsp_identity>12</Hsp_identity>\n+ <Hsp_positive>23</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>33</Hsp_align-len>\n+ <Hsp_qseq>KTHLRSHTGEKPYTCEYPGCSKAFSNASDRAKH</Hsp_qseq>\n+ <Hsp_hseq>RTHVRIHTGDRPFVCPFDACNKKFAQSTNLKSH</Hsp_hseq>\n+ <Hsp_midline>+TH+R HTG++P+ C + C+K F+ +++ H</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>70</Statistics_db-num>\n+ <Statistics_db-len>3333194</Statistics_db-len>\n+ <Statistics_hsp-len>96</Statistics_hsp-len>\n+ <Statistics_eff-space>1306438952</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n'

diff -r 000000000000 -r f493979f1408 test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml.bed Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,50 @@
+contig2 16199 18659 ci-PA 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 18939 20598 ci-PA 604 - 18939 20598 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig2 18712 18877 ci-PA 964 - 18712 18877 0 1 165, 0,
+contig1 31366 33826 ci-PA 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35765 ci-PA 604 - 34106 35765 0 7 510,210,432,84,63,45,174, 0,564,774,1278,1368,1434,1485,
+contig1 33879 34044 ci-PA 964 - 33879 34044 0 1 165, 0,
+contig24 12402 12561 ci-PA 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12570 ci-PA 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig24 3846 4032 ci-PA 0 - 3846 4032 0 3 51,21,96, 0,51,90,
+contig23 32405 32564 ci-PA 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32573 ci-PA 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig23 23849 24035 ci-PA 0 - 23849 24035 0 3 51,21,96, 0,51,90,
+contig67 20513 20759 ci-PA 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20531 20753 ci-PA 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,
+contig67 18177 18309 ci-PA 0 - 18177 18309 0 1 132, 0,
+contig67 20471 20660 ci-PA 0 - 20471 20660 0 1 189, 0,
+contig67 18201 18300 ci-PA 0 - 18201 18300 0 1 99, 0,
+contig66 35516 35762 ci-PA 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35534 35756 ci-PA 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig66 33180 33312 ci-PA 0 - 33180 33312 0 1 132, 0,
+contig66 35474 35663 ci-PA 0 - 35474 35663 0 1 189, 0,
+contig66 33204 33303 ci-PA 0 - 33204 33303 0 1 99, 0,
+contig2 18711 20598 ci-PC 584 - 18711 20598 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig2 18601 18889 ci-PC 0 - 18601 18889 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig1 33878 35765 ci-PC 584 - 33878 35765 0 8 99,510,210,432,84,63,48,171, 0,228,792,1002,1506,1596,1662,1716,
+contig1 33768 34056 ci-PC 0 - 33768 34056 0 5 63,36,51,54,45, 0,75,123,180,243,
+contig24 12468 12561 ci-PC 0 - 12468 12561 0 1 93, 0,
+contig23 32471 32564 ci-PC 0 - 32471 32564 0 1 93, 0,
+contig2 16199 18659 ci-PB 358 - 16199 18659 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig2 18939 20268 ci-PB 560 - 18939 20268 0 4 510,210,432,51, 0,564,774,1278,
+contig2 18712 18877 ci-PB 964 - 18712 18877 0 1 165, 0,
+contig1 31366 33826 ci-PB 358 - 31366 33826 0 18 126,114,27,174,186,84,69,45,204,108,117,144,123,150,24,48,495,165, 0,126,240,270,444,630,726,801,846,1056,1167,1290,1440,1566,1722,1746,1794,2295,
+contig1 34106 35435 ci-PB 560 - 34106 35435 0 4 510,210,432,51, 0,564,774,1278,
+contig1 33879 34044 ci-PB 964 - 33879 34044 0 1 165, 0,
+contig24 12402 12561 ci-PB 0 - 12402 12561 0 2 63,96, 0,63,
+contig24 12402 12570 ci-PB 0 - 12402 12570 0 4 21,42,90,15, 0,21,63,153,
+contig24 3846 4032 ci-PB 0 - 3846 4032 0 3 51,21,96, 0,51,90,
+contig23 32405 32564 ci-PB 0 - 32405 32564 0 2 63,96, 0,63,
+contig23 32405 32573 ci-PB 0 - 32405 32573 0 4 21,42,90,15, 0,21,63,153,
+contig23 23849 24035 ci-PB 0 - 23849 24035 0 3 51,21,96, 0,51,90,
+contig67 20513 20759 ci-PB 0 - 20513 20759 0 4 81,51,21,93, 0,81,132,153,
+contig67 20531 20753 ci-PB 0 - 20531 20753 0 4 111,24,51,36, 0,111,135,186,
+contig67 18177 18309 ci-PB 0 - 18177 18309 0 1 132, 0,
+contig67 20471 20660 ci-PB 0 - 20471 20660 0 1 189, 0,
+contig67 18201 18300 ci-PB 0 - 18201 18300 0 1 99, 0,
+contig66 35516 35762 ci-PB 0 - 35516 35762 0 4 81,51,21,93, 0,81,132,153,
+contig66 35534 35756 ci-PB 0 - 35534 35756 0 4 111,24,51,36, 0,111,135,186,
+contig66 33180 33312 ci-PB 0 - 33180 33312 0 1 132, 0,
+contig66 35474 35663 ci-PB 0 - 35474 35663 0 1 189, 0,
+contig66 33204 33303 ci-PB 0 - 33204 33303 0 1 99, 0,

diff -r 000000000000 -r f493979f1408 test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml.psl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tblastN/workflowInputs/tblastn_Dbia3_ci.xml.psl Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,50 @@
+1458 762 183 0 7 60 10 57 +- ci-PA 4191 1725 4188 contig2 45017 16199 18659 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1725,1890,2391,2448,2472,2622,2745,2889,3006,3114,3324,3369,3438,3528,3720,3894,3930,4062, 26358,26529,27024,27072,27102,27255,27384,27534,27654,27768,27972,28023,28104,28188,28374,28551,28578,28692,
+987 300 231 0 1 3 5 141 +- ci-PA 4191 39 1560 contig2 45017 18939 20598 7 174,45,63,84,432,210,510, 39,213,258,321,405,840,1050, 24419,24599,24647,24716,24872,25304,25568,
+162 3 0 0 0 0 0 0 +- ci-PA 4191 1560 1725 contig2 45017 18712 18877 1 165, 1560, 26140,
+1458 762 183 0 7 60 10 57 +- ci-PA 4191 1725 4188 contig1 45179 31366 33826 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1725,1890,2391,2448,2472,2622,2745,2889,3006,3114,3324,3369,3438,3528,3720,3894,3930,4062, 11353,11524,12019,12067,12097,12250,12379,12529,12649,12763,12967,13018,13099,13183,13369,13546,13573,13687,
+987 300 231 0 1 3 5 141 +- ci-PA 4191 39 1560 contig1 45179 34106 35765 7 174,45,63,84,432,210,510, 39,213,258,321,405,840,1050, 9414,9594,9642,9711,9867,10299,10563,
+162 3 0 0 0 0 0 0 +- ci-PA 4191 1560 1725 contig1 45179 33879 34044 1 165, 1560, 11135,
+69 90 0 0 1 6 0 0 +- ci-PA 4191 1467 1632 contig24 40010 12402 12561 2 96,63, 1467,1569, 27449,27545,
+78 90 0 0 3 15 0 0 +- ci-PA 4191 1542 1725 contig24 40010 12402 12570 4 15,90,42,21, 1542,1563,1659,1704, 27440,27455,27545,27587,
+63 105 0 0 1 6 1 18 +- ci-PA 4191 1536 1710 contig24 40010 3846 4032 3 96,21,51, 1536,1632,1659, 35978,36092,36113,
+69 90 0 0 1 6 0 0 +- ci-PA 4191 1467 1632 contig23 50012 32405 32564 2 96,63, 1467,1569, 17448,17544,
+78 90 0 0 3 15 0 0 +- ci-PA 4191 1542 1725 contig23 50012 32405 32573 4 15,90,42,21, 1542,1563,1659,1704, 17439,17454,17544,17586,
+63 105 0 0 1 6 1 18 +- ci-PA 4191 1536 1710 contig23 50012 23849 24035 3 96,21,51, 1536,1632,1659, 25977,26091,26112,
+87 159 0 0 3 12 0 0 +- ci-PA 4191 1530 1788 contig67 44531 20513 20759 4 93,21,51,81, 1530,1626,1653,1707, 23772,23865,23886,23937,
+87 135 0 0 3 18 0 0 +- ci-PA 4191 1437 1677 contig67 44531 20531 20753 4 36,51,24,111, 1437,1482,1536,1566, 23778,23814,23865,23889,
+48 84 0 0 0 0 0 0 +- ci-PA 4191 1503 1635 contig67 44531 18177 18309 1 132, 1503, 26222,
+69 120 0 0 0 0 0 0 +- ci-PA 4191 1458 1647 contig67 44531 20471 20660 1 189, 1458, 23871,
+36 63 0 0 0 0 0 0 +- ci-PA 4191 1602 1701 contig67 44531 18201 18300 1 99, 1602, 26231,
+87 159 0 0 3 12 0 0 +- ci-PA 4191 1530 1788 contig66 45011 35516 35762 4 93,21,51,81, 1530,1626,1653,1707, 9249,9342,9363,9414,
+87 135 0 0 3 18 0 0 +- ci-PA 4191 1437 1677 contig66 45011 35534 35756 4 36,51,24,111, 1437,1482,1536,1566, 9255,9291,9342,9366,
+48 84 0 0 0 0 0 0 +- ci-PA 4191 1503 1635 contig66 45011 33180 33312 1 132, 1503, 11699,
+69 120 0 0 0 0 0 0 +- ci-PA 4191 1458 1647 contig66 45011 35474 35663 1 189, 1458, 9348,
+36 63 0 0 0 0 0 0 +- ci-PA 4191 1602 1701 contig66 45011 33204 33303 1 99, 1602, 11708,
+1050 336 231 0 1 3 6 270 +- ci-PC 1716 39 1659 contig2 45017 18711 20598 8 171,48,63,84,432,210,510,99, 39,210,258,321,405,840,1050,1560, 24419,24596,24647,24716,24872,25304,25568,26207,
+111 138 0 0 0 0 4 39 +- ci-PC 1716 1467 1716 contig2 45017 18601 18889 5 45,54,51,36,63, 1467,1512,1566,1617,1653, 26128,26182,26242,26305,26353,
+1050 336 231 0 1 3 6 270 +- ci-PC 1716 39 1659 contig1 45179 33878 35765 8 171,48,63,84,432,210,510,99, 39,210,258,321,405,840,1050,1560, 9414,9591,9642,9711,9867,10299,10563,11202,
+111 138 0 0 0 0 4 39 +- ci-PC 1716 1467 1716 contig1 45179 33768 34056 5 45,54,51,36,63, 1467,1512,1566,1617,1653, 11123,11177,11237,11300,11348,
+45 48 0 0 0 0 0 0 +- ci-PC 1716 1467 1560 contig24 40010 12468 12561 1 93, 1467, 27449,
+45 48 0 0 0 0 0 0 +- ci-PC 1716 1467 1560 contig23 50012 32471 32564 1 93, 1467, 17448,
+1458 762 183 0 7 60 10 57 +- ci-PB 3837 1371 3834 contig2 45017 16199 18659 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1371,1536,2037,2094,2118,2268,2391,2535,2652,2760,2970,3015,3084,3174,3366,3540,3576,3708, 26358,26529,27024,27072,27102,27255,27384,27534,27654,27768,27972,28023,28104,28188,28374,28551,28578,28692,
+834 264 105 0 1 3 2 126 +- ci-PB 3837 0 1206 contig2 45017 18939 20268 4 51,432,210,510, 0,51,486,696, 24749,24872,25304,25568,
+162 3 0 0 0 0 0 0 +- ci-PB 3837 1206 1371 contig2 45017 18712 18877 1 165, 1206, 26140,
+1458 762 183 0 7 60 10 57 +- ci-PB 3837 1371 3834 contig1 45179 31366 33826 18 165,495,48,24,150,123,144,117,108,204,45,69,84,186,174,27,114,126, 1371,1536,2037,2094,2118,2268,2391,2535,2652,2760,2970,3015,3084,3174,3366,3540,3576,3708, 11353,11524,12019,12067,12097,12250,12379,12529,12649,12763,12967,13018,13099,13183,13369,13546,13573,13687,
+834 264 105 0 1 3 2 126 +- ci-PB 3837 0 1206 contig1 45179 34106 35435 4 51,432,210,510, 0,51,486,696, 9744,9867,10299,10563,
+162 3 0 0 0 0 0 0 +- ci-PB 3837 1206 1371 contig1 45179 33879 34044 1 165, 1206, 11135,
+69 90 0 0 1 6 0 0 +- ci-PB 3837 1113 1278 contig24 40010 12402 12561 2 96,63, 1113,1215, 27449,27545,
+78 90 0 0 3 15 0 0 +- ci-PB 3837 1188 1371 contig24 40010 12402 12570 4 15,90,42,21, 1188,1209,1305,1350, 27440,27455,27545,27587,
+63 105 0 0 1 6 1 18 +- ci-PB 3837 1182 1356 contig24 40010 3846 4032 3 96,21,51, 1182,1278,1305, 35978,36092,36113,
+69 90 0 0 1 6 0 0 +- ci-PB 3837 1113 1278 contig23 50012 32405 32564 2 96,63, 1113,1215, 17448,17544,
+78 90 0 0 3 15 0 0 +- ci-PB 3837 1188 1371 contig23 50012 32405 32573 4 15,90,42,21, 1188,1209,1305,1350, 17439,17454,17544,17586,
+63 105 0 0 1 6 1 18 +- ci-PB 3837 1182 1356 contig23 50012 23849 24035 3 96,21,51, 1182,1278,1305, 25977,26091,26112,
+87 159 0 0 3 12 0 0 +- ci-PB 3837 1176 1434 contig67 44531 20513 20759 4 93,21,51,81, 1176,1272,1299,1353, 23772,23865,23886,23937,
+87 135 0 0 3 18 0 0 +- ci-PB 3837 1083 1323 contig67 44531 20531 20753 4 36,51,24,111, 1083,1128,1182,1212, 23778,23814,23865,23889,
+48 84 0 0 0 0 0 0 +- ci-PB 3837 1149 1281 contig67 44531 18177 18309 1 132, 1149, 26222,
+69 120 0 0 0 0 0 0 +- ci-PB 3837 1104 1293 contig67 44531 20471 20660 1 189, 1104, 23871,
+36 63 0 0 0 0 0 0 +- ci-PB 3837 1248 1347 contig67 44531 18201 18300 1 99, 1248, 26231,
+87 159 0 0 3 12 0 0 +- ci-PB 3837 1176 1434 contig66 45011 35516 35762 4 93,21,51,81, 1176,1272,1299,1353, 9249,9342,9363,9414,
+87 135 0 0 3 18 0 0 +- ci-PB 3837 1083 1323 contig66 45011 35534 35756 4 36,51,24,111, 1083,1128,1182,1212, 9255,9291,9342,9366,
+48 84 0 0 0 0 0 0 +- ci-PB 3837 1149 1281 contig66 45011 33180 33312 1 132, 1149, 11699,
+69 120 0 0 0 0 0 0 +- ci-PB 3837 1104 1293 contig66 45011 35474 35663 1 189, 1104, 9348,
+36 63 0 0 0 0 0 0 +- ci-PB 3837 1248 1347 contig66 45011 33204 33303 1 99, 1248, 11708,

diff -r 000000000000 -r f493979f1408 test-data/trfBig/hubaInputs/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/hubaInputs/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/trfBig/hubaInputs/dbia3_trfBig_sorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/hubaInputs/dbia3_trfBig_sorted.bed Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,602 @@\n+contig1\t9130\t9428\ttrf\t163\t1.8\t164\t86\t2\t438\t36\t12\t13\t37\t1.82\tAAAAAAAATTATATCTTCGGTGTTTTTCAACATACAACCTCCTAAGCTTGGAAATAACATTTCTTAATCAGTTCTGAATTTCGAATTAAATTTTTATCAAAATCGGACAACTATACCATATAGCTGTCATAGGAAGGATTGGATAATTAGTGGTAAAATAATAT\n+contig1\t15707\t15757\ttrf\t20\t2.5\t19\t83\t9\t55\t32\t12\t2\t54\t1.49\tTATATCATTTATATCTCAG\n+contig1\t16261\t16302\ttrf\t12\t3.4\t12\t89\t0\t64\t2\t36\t24\t36\t1.69\tTCCGTCTGTCCG\n+contig1\t23387\t23483\ttrf\t45\t2.2\t45\t92\t1\t158\t19\t22\t30\t27\t1.98\tTCGGCGAAGAAATGTGCCACTTCGGCGGCACTTCTTGGAGTCACT\n+contig1\t23451\t23520\ttrf\t24\t2.9\t24\t80\t0\t75\t15\t26\t27\t30\t1.96\tTTCGGCGACACTTCTTGAAGTCAG\n+contig1\t24200\t24233\ttrf\t15\t2.2\t15\t94\t0\t57\t51\t12\t15\t21\t1.75\tAAACAATGGAATGCT\n+contig1\t29159\t29628\ttrf\t162\t2.9\t160\t80\t8\t518\t37\t12\t11\t38\t1.80\tGGAAAACATGAAATAAAAATTATATCTTTCGTGTTTTTTAACATATACCTTCTAAGCTTGAAAATAACATTTTTTATTTGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGTCATAGGAACAATCGGAAAATAAGTA\n+contig1\t37571\t37606\ttrf\t8\t4.4\t8\t88\t0\t52\t31\t25\t42\t0\t1.55\tGACGGACA\n+contig1\t38436\t38491\ttrf\t12\t4.6\t12\t81\t0\t65\t0\t38\t27\t34\t1.57\tTGTCCGTCCGTC\n+contig1\t38436\t38491\ttrf\t20\t3.1\t18\t80\t17\t69\t0\t38\t27\t34\t1.57\tTGTCCGTCTGTCCGTCCG\n+contig1\t38436\t38491\ttrf\t8\t6.9\t8\t79\t8\t58\t0\t38\t27\t34\t1.57\tTGTCCGTC\n+contig1\t43116\t43168\ttrf\t2\t26.0\t2\t96\t0\t95\t48\t0\t1\t50\t1.12\tTA\n+contig10\t7159\t7189\ttrf\t13\t2.3\t13\t94\t0\t51\t36\t10\t16\t36\t1.82\tAATGATGCATTTA\n+contig10\t7363\t7540\ttrf\t101\t1.8\t95\t85\t7\t246\t44\t9\t10\t36\t1.70\tTTTTTATAAAATTGAATTCGAAATTCAGAACCAATTAAAAAATATTATTTATAAGAAGGTTATATGTTAAAAAACACAGTCGATATGATATAGTC\n+contig10\t8034\t8065\ttrf\t16\t1.9\t16\t93\t0\t53\t38\t25\t35\t0\t1.56\tACAGACAGACGGACGA\n+contig10\t16407\t16472\ttrf\t24\t2.7\t24\t88\t4\t87\t23\t23\t33\t20\t1.97\tGAAGTGTCGCCGAAGTGACTCCTG\n+contig10\t17443\t17508\ttrf\t24\t2.7\t24\t88\t4\t87\t23\t24\t33\t18\t1.96\tGAAGTGTCGCCGAAGTGACTCCTG\n+contig10\t18419\t18897\ttrf\t162\t3.0\t162\t78\t8\t408\t35\t15\t12\t36\t1.85\tCCCAAAGATAATTTTTCCATATTATTTTACCACTAATTTTCCGATCCTTCATATGGCAGCAATATGATATAGTCATCCGATTTCGATAAAAATTGAATTCAAAATTCAGAACTAATTAAAAATGGTTATATCCAAGCTTAGAAAGCTATATGTTAAAAATAA\n+contig10\t28438\t28868\ttrf\t163\t2.7\t160\t78\t7\t465\t38\t12\t13\t35\t1.82\tAACATTTTTTAATTAGTTCTGAATTTAAATTTAAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAATAAAAAAATTATATCTTCGGTGTTTTTAACATATAACTCCAAAGCTTAAAAAT\n+contig10\t32277\t32320\ttrf\t2\t21.5\t2\t95\t0\t77\t48\t0\t0\t51\t1.00\tAT\n+contig10\t34149\t34186\ttrf\t19\t1.9\t19\t94\t0\t65\t32\t13\t37\t16\t1.87\tGCTGAGGATGAGATACAGA\n+contig11\t7433\t7863\ttrf\t163\t2.7\t160\t78\t7\t465\t38\t12\t13\t35\t1.82\tAACATTTTTTAATTAGTTCTGAATTTAAATTTAAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAATAAAAAAATTATATCTTCGGTGTTTTTAACATATAACTCCAAAGCTTAAAAAT\n+contig11\t11272\t11315\ttrf\t2\t21.5\t2\t95\t0\t77\t48\t0\t0\t51\t1.00\tAT\n+contig11\t13144\t13181\ttrf\t19\t1.9\t19\t94\t0\t65\t32\t13\t37\t16\t1.87\tGCTGAGGATGAGATACAGA\n+contig11\t22738\t22776\ttrf\t20\t1.9\t20\t88\t0\t58\t34\t13\t7\t44\t1.72\tTATATATATAGAACCTGTTC\n+contig11\t25115\t25366\ttrf\t138\t1.8\t138\t95\t0\t457\t36\t13\t9\t40\t1.77\tCAAATTTTTTGTTTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATAACGTTATAAAAAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAACAAGAATACCTTTTGTTTACATTTTAC\n+contig11\t25870\t25921\ttrf\t18\t2.8\t18\t91\t5\t77\t25\t23\t0\t50\t1.49\tTCATCTATATCTTTCATA\n+contig11\t25872\t25939\ttrf\t23\t2.9\t23\t75\t6\t64\t23\t22\t1\t52\t1.56\tATCTTTCATTTCATATCATCTAT\n+contig11\t31165\t31562\ttrf\t159\t2.5\t155\t82\t6\t458\t38\t12\t13\t35\t1.82\tTTTTGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGCCATAGAACGATCGGAAAATTAGTGGAAAATATAAAAAAATTATATCTTCGGTGACTTTAACATATAACTTCCAATACTTGAAAATACAATTTTTAATTAGTTCTAAA\n+contig12\t2269\t2312\ttrf\t2\t21.5\t2\t95\t0\t77\t48\t0\t0\t51\t1.00\tAT\n+contig12\t4141\t4178\ttrf\t19\t1.9\t19\t94\t0\t65\t32\t13\t37\t16\t1.87\tGCTGAGGATGAGATACAGA\n+contig12\t13735\t13773\ttrf\t20\t1.9\t20\t88\t0\t58\t34\t13\t7\t44\t1.72\tTATATATATAGAACCTGTTC\n+contig12\t16112\t16363\ttrf\t138\t1.8\t138\t95\t0\t457\t36\t13\t9\t40\t1.77\tCAAATTTTTTGTTTAAAACCGTTTTGGACTCTAAGGCTATGCAATGCATATAACGTTATAAAAAAAGTATTTACTTTTTTAACAAATTTATAACTTACCTATAACATATAACAAGAATACCTTTTGTTTACATTTTAC\n+contig12\t16867\t16918\ttrf\t18\t2.8\t18\t91\t5\t77\t25\t23\t0\t50\t1.49\tTCATCTATATCTTTCATA\n+contig12\t16869\t16936\ttrf\t23\t2.9\t23\t75\t6\t64\t23\t22\t1\t52\t1.56\tATCTTTCATTTCATATCATCTAT\n+contig12\t22162\t22559\ttrf\t159\t2.5\t155\t82\t6\t458\t38\t12\t13\t35\t1.82\tTTTTGAATTAAATTTTATCA'..b'AAAAATTATATCCTTGGTATTTTTTAACATATAACAATATAAGCTAGAAAAG\n+contig70\t17962\t18295\ttrf\t161\t2.1\t160\t83\t5\t413\t37\t12\t13\t35\t1.84\tAAAAAATTATATCTCTGGTGTTTTTAAACATATAACCTCCTAAACTTGGAAATAACATTTTATAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAACCCGACGACTATATCATACATGTAACTGTAACGATCGGAAAATTGATGGGAAAATAATATG\n+contig70\t19030\t19306\ttrf\t137\t2.0\t137\t94\t1\t482\t39\t13\t13\t34\t1.83\tTTTAACACATACCTTTCTAAGCTTGGATATAACATTTTTAAACTGGTTCTGAATTTCAAATTAAATTCAATTAAAATCGGACGACTATATCATATAGCTCCCATAGGAAAAATCGGAAAATTAGTGAGAAAATAATA\n+contig70\t22269\t22308\ttrf\t19\t2.1\t19\t100\t0\t78\t58\t15\t15\t10\t1.62\tAACTAAGGAAATACCAGAA\n+contig70\t22812\t23252\ttrf\t162\t2.8\t156\t84\t5\t562\t37\t11\t13\t37\t1.81\tTTCTAAGCTTGAAATAACATTTTTTAATTAGTTCTGAATTTCGAATTTAATTTTATTAAAATCGGACGACTATATCATATAGCTGCCATAGGAACGATCGGAAAATTAGTGGAAAATAATAAATAAAAATTATATTTGTATTTTTAACATATAACC\n+contig70\t23421\t23486\ttrf\t13\t4.7\t13\t70\t20\t51\t38\t0\t0\t61\t0.96\tATATATATAATTT\n+contig70\t23426\t23479\ttrf\t7\t7.4\t7\t79\t12\t54\t35\t0\t0\t64\t0.94\tTATATTT\n+contig70\t23430\t23486\ttrf\t27\t2.0\t27\t83\t10\t69\t35\t0\t0\t64\t0.94\tATTTATATATTTATTAATATATTTTAT\n+contig70\t25576\t25606\ttrf\t12\t2.5\t12\t94\t0\t51\t33\t26\t36\t3\t1.73\tACGGACGGACAG\n+contig70\t27263\t27382\ttrf\t63\t1.9\t63\t85\t3\t168\t27\t25\t21\t26\t1.99\tATTTTTCCAAGCACTTTCCTGTACAAGGGAAACGTCCCAGGGAAAGCCTATCGGAATTTCAAA\n+contig70\t27353\t27406\ttrf\t25\t2.1\t25\t85\t0\t70\t30\t26\t32\t11\t1.91\tGGAAACGTCCCAGGGAAAGCCCATC\n+contig70\t27848\t27878\ttrf\t12\t2.5\t12\t88\t0\t51\t30\t30\t40\t0\t1.57\tACGGACGGACAG\n+contig70\t35504\t35713\ttrf\t102\t2.0\t102\t99\t0\t409\t37\t12\t13\t36\t1.82\tAAAACGATGGTAGACAAATATGCATATATTTTTTACACAAAACGAAATATAATGGACTTTTAAAAATTCTTTTTTCTATCTTTCCTGGTGGGAGATATATAT\n+contig70\t43333\t43446\ttrf\t57\t2.0\t57\t94\t0\t199\t30\t17\t22\t29\t1.97\tAATATTGGGAATAACATATTATCTTATAATATGGGAGCGCGAAGGCTCCTCGCCCAT\n+contig70\t44241\t44281\ttrf\t13\t2.9\t14\t85\t7\t55\t27\t22\t12\t37\t1.90\tCTACATGTTACATG\n+contig70\t44242\t44281\ttrf\t7\t5.7\t7\t81\t6\t53\t28\t20\t12\t38\t1.89\tTACATGT\n+contig70\t44485\t44531\ttrf\t14\t3.3\t14\t84\t0\t65\t41\t21\t10\t26\t1.86\tAACCGTATATGACT\n+contig70\t45147\t45181\ttrf\t16\t2.0\t17\t88\t11\t52\t52\t0\t2\t44\t1.16\tAAATATTAGTAATATAT\n+contig70\t46706\t46990\ttrf\t147\t1.9\t147\t100\t0\t568\t39\t10\t9\t40\t1.72\tTTCTTTATTTTTTTTATTTTAAAATACTTAGTACTTAGTAATGTCGCTAAAACCAATATAATATTCTTTAAAATTTAGAAAATATATTCAGACTTCGAATTACAAGGTGTATTAGAAGATAAATTAAACTCTAAAGCTTAATTTATC\n+contig70\t53900\t53978\ttrf\t28\t2.8\t28\t80\t5\t97\t15\t43\t5\t35\t1.69\tCTCTGTCACCCTCTCTTTACCTACCTCA\n+contig8\t2833\t2903\ttrf\t24\t2.9\t25\t83\t8\t92\t15\t27\t27\t30\t1.96\tCTTCGGCGACACTTCTTGGAAGTCA\n+contig8\t22744\t22922\ttrf\t88\t2.0\t88\t97\t0\t338\t28\t16\t24\t30\t1.96\tATGGGAGCTATAAGATATAGTTGTCCCATCCGGCAGGTTTCGACTTATATATTGCCTGCCATAGAAAGGAAACTTTTGGGAAAGTTTC\n+contig8\t29631\t30109\ttrf\t162\t3.0\t159\t81\t4\t573\t36\t12\t14\t36\t1.84\tAAAAATTATATCTTCGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACAATTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGCCATAGGAACAATCGGAAAATTAGTGGAAAATGAAAT\n+contig9\t2833\t2903\ttrf\t24\t2.9\t25\t83\t8\t92\t15\t27\t27\t30\t1.96\tCTTCGGCGACACTTCTTGGAAGTCA\n+contig9\t22744\t22922\ttrf\t88\t2.0\t88\t97\t0\t338\t28\t16\t24\t30\t1.96\tATGGGAGCTATAAGATATAGTTGTCCCATCCGGCAGGTTTCGACTTATATATTGCCTGCCATAGAAAGGAAACTTTTGGGAAAGTTTC\n+contig9\t29631\t30109\ttrf\t162\t3.0\t159\t81\t4\t573\t36\t12\t14\t36\t1.84\tAAAAATTATATCTTCGGTGTTTTTTAACATATAACCTTCTAAGCTTGGAAATAACAATTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGCCATAGGAACAATCGGAAAATTAGTGGAAAATGAAAT\n+contig9\t37064\t37094\ttrf\t12\t2.5\t12\t100\t0\t60\t0\t40\t26\t33\t1.57\tGTCCGTCTGTCC\n+contig9\t37275\t37670\ttrf\t162\t2.4\t160\t82\t10\t455\t37\t12\t13\t35\t1.83\tATAACAATTTTTATTTGTTTTGAATTTCGAATTAAATTTATCAAAATCGGACGACTATATCATATAGCTGCCAAGAGAAACAATCGGAAAATTAGTGGAAAAATAACATTGAAAAAGTATATCTTCGGTGTTTCTTAACATACAACCTCATAAGCTTGAA\n+contig9\t37280\t37752\ttrf\t161\t2.9\t161\t80\t6\t492\t37\t11\t15\t35\t1.84\tATTTTTTAATTAGTTCTGAATTTCGAATTAAATTTTATCAAAATCGGACGACTATATCATATAGCTGCAATAGGAACAATCGGAAAATTAGTGGGAAATACATGTGAAAAAATTATATCTTTGGTGTTTTTAACATATAACCTTATAAGCTTGGAAATACA\n+contig9\t56173\t56203\ttrf\t13\t2.3\t13\t94\t0\t51\t36\t10\t16\t36\t1.82\tAATGATGCATTTA\n+contig9\t56377\t56554\ttrf\t101\t1.8\t95\t85\t7\t246\t44\t9\t10\t36\t1.70\tTTTTTATAAAATTGAATTCGAAATTCAGAACCAATTAAAAAATATTATTTATAAGAAGGTTATATGTTAAAAAACACAGTCGATATGATATAGTC\n+contig9\t57048\t57079\ttrf\t16\t1.9\t16\t93\t0\t53\t38\t25\t35\t0\t1.56\tACAGACAGACGGACGA\n'

diff -r 000000000000 -r f493979f1408 test-data/trfBig/output/dbia3_trfBig.bb

Binary file test-data/trfBig/output/dbia3_trfBig.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/trfBig/workflowInputs/dbia3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/workflowInputs/dbia3.fa Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/trfBig/workflowInputs/dbia3.fa.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/workflowInputs/dbia3.fa.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/trfBig/workflowInputs/dbia3_trfBig_unsorted.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/workflowInputs/dbia3_trfBig_unsorted.bed Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/trfBig/workflowInputs/dbia3_trfBig_unsorted_withMaskedGenome.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trfBig/workflowInputs/dbia3_trfBig_unsorted_withMaskedGenome.fa Wed Dec 21 12:13:04 2016 -0500

b'@@ -0,0 +1,66784 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diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,68 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1193.dat
+DEBUG:root:data_value: {u'index': u'/home/svc_galaxy/new/galaxy/database/files/_metadata_files/000/metadata_77.dat', u'order_index': u'11', u'name': u'HISAT2_Accepted_Hits', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1188.dat
+DEBUG:root:data_value: {u'order_index': u'21', u'name': u'Multi-Fasta_GlimmerHMM_Gene_Predictions', u'track_color': u'#000000', u'group_name': u'Other group'}
+DEBUG:root:Calling gff3ToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpC7M6B_.sorted.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
+DEBUG:root:data_value: {u'order_index': u'20', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Other group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpirJDCW.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmppQM471.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<Bam.Bam object at 0x1b78b90>, <BigWig.BigWig object at 0x1b78e10>, <Gtf.Gtf object at 0x1b78e90>, <Gff3.Gff3 object at 0x1b78e50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track HISAT2_Accepted_Hits.bam (in group default_group)
+DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group other_group)
+DEBUG:root:We DON'T add in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/915/dataset_1283_files/myHub/Dbia3/groups.txt the group Other group
+DEBUG:root:We just added track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb (in group other_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/Dbia3.2bit

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+
+name other_group
+label Other group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,44 @@
+    track HISAT2_Accepted_Hits.bam
+    longLabel HISAT2 Accepted Hits.bam
+    shortLabel HISAT2 Accepted
+    bigDataUrl tracks/HISAT2_Accepted_Hits.bam
+    type bam
+    visibility pack
+    thickDrawItem off
+    priority 11
+    color 0,0,0
+    group default_group
+
+    track RNA-Seq_Alignment_Summary.bigwig
+    longLabel RNA-Seq Alignment Summary
+    shortLabel RNA-Seq Alignme
+    bigDataUrl tracks/RNA-Seq_Alignment_Summary.bigwig
+    type bigWig
+    visibility full
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+
+    track StringTie_Assembled_Transcripts.bb
+    longLabel StringTie Assembled Transcripts
+    shortLabel StringTie Assem
+    bigDataUrl tracks/StringTie_Assembled_Transcripts.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 20
+    color 0,0,0
+    group other_group
+
+    track Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+    longLabel Multi-Fasta GlimmerHMM Gene Predictions
+    shortLabel Multi-Fasta Gli
+    bigDataUrl tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 21
+    color 0,0,0
+    group other_group
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/two_groups_multiple_tracks/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,82 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai">HISAT2_Accepted_Hits.bam.bai</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam">HISAT2_Accepted_Hits.bam</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb">Multi-Fasta_GlimmerHMM_Gene_Predictions.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_no_track/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_no_track/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

diff -r 000000000000 -r f493979f1408 test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit

Binary file test-data/two_groups_no_track/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_no_track/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_no_track/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_no_track/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_no_track/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/two_groups_no_track/two_groups_no_track_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_no_track/two_groups_no_track_trackhub.html Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,42 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1197.dat
+DEBUG:root:data_value: {u'order_index': u'20', u'name': u'StringTie_Assembled_Transcripts', u'track_color': u'#000000', u'group_name': u'Other group'}
+DEBUG:root:Calling gtfToGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling genePredToBigGenePred:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:sorted_bed_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmpqNltxC.sortedBed.bigGenePred
+DEBUG:root:chrom_sizes_file_name: /home/svc_galaxy/new/galaxy/database/tmp/tmplv6Lna.chrom.sizes
+DEBUG:root:big_bed_file_name: /home/svc_galaxy/new/galaxy/database/jobs_directory/000/914/dataset_1282_files/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb
+DEBUG:root:typeOption: bed12+8
+DEBUG:root:autoSql: /home/svc_galaxy/new/shed_tools/toolshed.g2.bx.psu.edu/repos/rmarenco/hubarchivecreator/d786bca6a75d/hubarchivecreator/bigGenePred.as
+DEBUG:root:tab option: True
+DEBUG:root:Calling bedToBigBed:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0x2d26d10>, <Gtf.Gtf object at 0x2d26d50>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/914/dataset_1282_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/914/dataset_1282_files/myHub/Dbia3/groups.txt the group Other group
+DEBUG:root:We just added track StringTie_Assembled_Transcripts.bb (in group other_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit

Binary file test-data/two_groups_one_track_both/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,10 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+
+name other_group
+label Other group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,22 @@
+    track RNA-Seq_Alignment_Summary.bigwig
+    longLabel RNA-Seq Alignment Summary
+    shortLabel RNA-Seq Alignme
+    bigDataUrl tracks/RNA-Seq_Alignment_Summary.bigwig
+    type bigWig
+    visibility full
+    thickDrawItem off
+    priority 10
+    color 0,0,0
+    group default_group
+
+    track StringTie_Assembled_Transcripts.bb
+    longLabel StringTie Assembled Transcripts
+    shortLabel StringTie Assem
+    bigDataUrl tracks/StringTie_Assembled_Transcripts.bb
+    type bigGenePred
+    visibility dense
+    thickDrawItem off
+    priority 20
+    color 0,0,0
+    group other_group
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig

Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb

Binary file test-data/two_groups_one_track_both/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_both/two_groups_one_track_both_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,73 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb">StringTie_Assembled_Transcripts.bb</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/__main__.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/__main__.log Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,20 @@
+DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
+
+DEBUG:root:Calling faToTwoBit:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling twoBitInfo:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:Calling sort:
+DEBUG:root:---------
+DEBUG:root:
+DEBUG:root:input_false_path: /home/svc_galaxy/new/galaxy/database/files/001/dataset_1195.dat
+DEBUG:root:data_value: {u'order_index': u'10', u'name': u'RNA-Seq_Alignment_Summary', u'track_color': u'#000000', u'group_name': u'Default group'}
+DEBUG:root:----- End of all_datatype_dictionary processing -----
+DEBUG:root:all_datatype_ordered_dictionary keys are: [<BigWig.BigWig object at 0xf57cd0>]
+DEBUG:root:----- Beginning of Track adding processing -----
+DEBUG:root:We just added in /home/svc_galaxy/new/galaxy/database/jobs_directory/000/913/dataset_1281_files/myHub/Dbia3/groups.txt the group Default group
+DEBUG:root:We just added track RNA-Seq_Alignment_Summary.bigwig (in group default_group)
+DEBUG:root:----- End of Track adding processing -----
+DEBUG:root:#### End of HubArchiveCreator Debug Mode: Bye! ####

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit

Binary file test-data/two_groups_one_track_first/myHub/Dbia3/Dbia3.2bit has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/myHub/Dbia3/groups.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,5 @@
+name default_group
+label Default group
+priority 2
+defaultIsClosed 0
+

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/myHub/Dbia3/trackDb.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig

Binary file test-data/two_groups_one_track_first/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig has changed

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/genomes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/myHub/genomes.txt Wed Dec 21 12:13:04 2016 -0500

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/myHub/hub.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/myHub/hub.txt Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+hub gonrampDbia3
+shortLabel Dbia3
+longLabel Dbia3
+genomesFile genomes.txt
+email rmarenco@gwu.edu
+descriptionUrl Dbia3.html

diff -r 000000000000 -r f493979f1408 test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/two_groups_one_track_first/two_groups_one_track_first_trackhub.html Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,70 @@
+
+<html>
+    <body>
+        <p>
+            The following has been generated by Hub Archive Creator:
+        </p>
+        <ul>
+
+                <li>
+                    myHub
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3.html">Dbia3.html</a>
+                </li>
+                <li>
+                    <a href="myHub/genomes.txt">genomes.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/hub.txt">hub.txt</a>
+                </li>
+                <li>
+                    Dbia3
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/groups.txt">groups.txt</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a>
+                </li>
+                <li>
+                    <a href="myHub/Dbia3/description.html">description.html</a>
+                </li>
+                <li>
+                    tracks
+                </li>
+                <ul>
+
+                <li>
+                    <a href="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig">RNA-Seq_Alignment_Summary.bigwig</a>
+                </li>
+
+                </ul>
+                <li>
+                    <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a>
+                </li>
+
+                </ul>
+
+                </ul>
+                <li>
+                    .
+                </li>
+                <ul>
+
+                <li>
+                    <a href="./__main__.log">__main__.log</a>
+                </li>
+
+                </ul>
+
+        </ul>
+    </body>
+</html>
+
+
+

diff -r 000000000000 -r f493979f1408 todo.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/todo.md Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,50 @@
+# HubArchiveCreator's TODO
+
+*TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
+
+### TO COMPLETE
+
+
+- [ ] Parse the [JSON received from Galaxy inputs](hubArchiveCreator.xml#L47-L137) in a class instead of doing [this spaghetti code](hubArchiveCreator.py#L137-L149)
+- [ ] Don't let the Tool Classes manage the archive (add or remove files / folders) => Everything should pass through TrackHub or another class dedicated to that
+- [ ] Move the class and others program related files, into separated folders
+- [ ] Take into account the name of the reference genome / the change:
+ - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
+- [ ] Replace Gff3/GTF by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
+- [ ] Manage the error when a user is selecting Generic Bed instead of Bed Simple Repeats. Two options: a. Output a better error message ("Check with the other Bed options") b. Identify internally this is not a regular BED but a specific one
+- [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
+- [ ] Rename all occurences of `extension` with `datatype`
+- [ ] Follow https://google.github.io/styleguide/pyguide.html
+- [ ] Migrate to Python 3
+- [ ] Remove the repetition of the extension file if it already exists
+- [ ] Better thinking about the tool_directory management / Classes path refactoring
+
+### DONE
+
+
+- [x] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
+- [x] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
+- [x] Add a debug mode to have more outputs
+- [x] Improve the standard output of HAC
+- [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
+- [x] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
+- [x] Sort the order of the HTML directories/files
+- [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py
+- [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
+- [x] Add a script to install the huba datatype
+- [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py
+- [x] Fix the errors for the stdio regexp not properly processed in error case (always green) => Used `detect_errors` in galaxy wrapper and raise Exception in Python
+- [x] Add a class named ~~TrfBigProcess~~ BedSimpleRepeats
+- [x] Add a class named TrackHub: Create the base TrackHub hierarchy
+- [x] Change the Name of the classes
+- [x] Add a class named AugustusProcess: Process the Augustus output to BigBed (and others needed in TrackHub) and (create folders + add the files into the right location => Process can be ported in a class responsible for that)
+ - [x] Add a class named AugustusProcess
+ - [x] Process the Augustus output to BigBed
+ - [x] create folders + add the files into the right location
+ - [x] Creation of folders to be ported into a separated class => In Datatype.py but should be into a dedicated to file manipulation class
+ - [x] Refactoring of the AugustusProcess class to behave like a class and not like a procedural masked into a class
+ - [x] Rename AugustusProcess into something more generic if the process is shared (gtf to BigBed) => Gff3.py
+- [x] Use gffToBed for Gtf instead of GtfToGenePred => Cancelled
+- [x] Clean the mess with the File handling (sometimes File, sometimes String, sometimes open File)
+- [x] Find a way to avoid repetitions in TrackDb and Track (I repeat myself atm) => Track instance has a TrackDb instance as attribute
+- [x] Refactor the creation of the structure to TrackHub: Access to paths via this Class, and creation of file through it

diff -r 000000000000 -r f493979f1408 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,132 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    
+    
+    <package name="ucsc_tools" version="312">
+        <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+
+    
+    
+
+
+    
+    <package name="gff3ToGenePred" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
+                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    
+    <package name="gtfToGenePred" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
+                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    
+    <package name="genePredToBed" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
+                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred
+
+    
+    <package name="genePredToBigGenePred" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+
+    
+    <package name="pslToBigPsl" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
+</tool_dependency>

diff -r 000000000000 -r f493979f1408 trackHub/README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trackHub/README.md Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,12 @@
+This folder exists to configure Galaxy to handle the files generated by HubArchiveCreator tool
+
+* The **content** of datatypes_conf.xml should go inside config/datatypes_conf.xml, under \<registration\> (Copy config/datatypes_conf.xml.sample to config/datatypes_conf.xml if it does not exist yet)
+* The content of tracks_partial.py should go inside `lib/galaxy/datatypes/tracks.py`
+* trackhub.xml should go inside display_application/ucsc/
+
+
+TODO:
+
+- [x] Create a script to copy all these files directly into galaxy => Done but not usable now I have changed the datatype to match Galaxy IUC
+- [ ] Need to modify the script `util/add_datatype.py` to match the changes introduced in https://github.com/galaxyproject/galaxy/pull/2348
+- [x] Create a package in ToolShed that install directly this when installing HubArchiveCreator => Not recommended by Galaxy IUC and team

diff -r 000000000000 -r f493979f1408 trackHub/datatypes_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trackHub/datatypes_conf.xml Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,3 @@
+<datatype extension="trackhub" type="galaxy.datatypes.tracks:UCSCTrackHub" display_in_upload="true">
+ <display file="ucsc/trackhub.xml" />
+</datatype>

diff -r 000000000000 -r f493979f1408 trackHub/trackhub.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trackHub/trackhub.xml Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,6 @@
+<display id="ucsc_trackhub" version="1.0.0" name="display at Track Hub UCSC">
+    <link id="main" name="main">
+        <url>https://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=${qp($hub_file.url + '/myHub/hub.txt')}&hgHub_do_firstDb=on&hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on</url>
+        <param type="data" name="hub_file" url="galaxy_${DATASET_HASH}" allow_extra_files_access="True" />
+    </link>
+</display>

diff -r 000000000000 -r f493979f1408 trackHub/tracks_partial.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trackHub/tracks_partial.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,87 @@
+"""
+HubAssembly datatype
+"""
+import logging
+
+from galaxy.datatypes.text import Html
+
+log = logging.getLogger( __name__ )
+
+# !!! README !!! The content of this file should be added in tracks.py, but do it carefully!
+# Don't erase the existing content
+
+
+class UCSCTrackHub( Html ):
+    """
+    derived class for BioC data structures in Galaxy
+    """
+
+    file_ext = 'trackhub'
+    composite_type = 'auto_primary_file'
+
+    def __init__( self, **kwd ):
+        Html.__init__( self, **kwd )
+
+    def generate_primary_file( self, dataset=None ):
+        """
+        This is called only at upload to write the html file
+        cannot rename the datasets here - they come with the default unfortunately
+        """
+        rval = [
+            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
+            This composite dataset is composed of the following files:<p/><ul>' % (
+                self.file_ext)]
+
+        def create_tree(path, tree):
+            if path[0] in tree:
+                create_tree(path[1:], tree[path[0]])
+            else:
+                tree[path[0]] = {}
+                if len(path) == 1:
+                    return
+                else:
+                    create_tree(path[1:], tree[path[0]])
+
+        def print_tree(tree, level):
+            if len(tree) == 0:
+                return
+
+            for vertex in tree:
+                    composite_name = vertex
+                    bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name)
+                    rval.append(bullet_point)
+                    # Parent, so need to create a sub <ul>
+                    if len(tree[vertex]) > 0:
+                        rval.append('<ul>')
+                        print_tree(tree[vertex], level+1)
+                        rval.append('</ul>')
+
+        walkable_tree = {}
+
+        for composite_name_full_path, composite_file in self.get_composite_files(dataset=dataset).iteritems():
+            paths = composite_name_full_path.split('/')
+            # Prepare the tree from to perform a Depth First Search
+            create_tree(paths, walkable_tree)
+
+        # Perform a Depth First Search to print all the directory and files properly
+        print_tree(walkable_tree, 0)
+
+        # rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
+        rval.append('</ul></html>')
+        return "\n".join(rval)
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Track Hub structure: Visualization in UCSC Track Hub"
+
+    def sniff( self, filename ):
+        return False

diff -r 000000000000 -r f493979f1408 trf_simpleRepeat.as
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trf_simpleRepeat.as Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,20 @@
+table simpleRepeat
+"Describes the Simple Tandem Repeats"
+   (
+   string chrom;       "Reference sequence chromosome or scaffold"
+   uint   chromStart; "Start position in chromosome"
+   uint   chromEnd;    "End position in chromosome"
+   string name;        "Simple Repeats tag name"
+   uint   period;      "Length of repeat unit"
+   float  copyNum;     "Mean number of copies of repeat"
+   uint   consensusSize; "Length of consensus sequence"
+   uint   perMatch;   "Percentage Match"
+   uint   perIndel;   "Percentage Indel"
+   uint   score; "Alignment Score = 2*match-7*mismatch-7*indel; minscore=50"
+   uint   A;   "Percent of A's in repeat unit"
+   uint   C;   "Percent of C's in repeat unit"
+   uint   G;   "Percent of G's in repeat unit"
+   uint   T;   "Percent of T's in repeat unit"
+   float   entropy;   "Entropy"
+   lstring sequence;     "Sequence of repeat unit element"
+   )

diff -r 000000000000 -r f493979f1408 util/Fasta.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/Fasta.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,16 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Class describing the Fasta format
+(As of the 07/20/2016, only used with the reference genome)
+"""
+
+class Fasta(object):
+    def __init__(self, false_path, name, assembly_id):
+        self.false_path = false_path
+        self.name = name
+
+        if not assembly_id:
+            assembly_id = "unknown"
+        self.assembly_id = assembly_id
\ No newline at end of file

diff -r 000000000000 -r f493979f1408 util/Fasta.pyc

Binary file util/Fasta.pyc has changed

diff -r 000000000000 -r f493979f1408 util/Filters.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/Filters.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,9 @@
+import logging
+
+class TraceBackFormatter(logging.Formatter):
+    def format(self, record):
+        # If the log has some Exception text, we don't display them
+        s = super(TraceBackFormatter, self).format(record)
+        if record.exc_text or record.exc_info:
+            s = record.message
+        return s

diff -r 000000000000 -r f493979f1408 util/Filters.pyc

Binary file util/Filters.pyc has changed

diff -r 000000000000 -r f493979f1408 util/__init__.pyc

Binary file util/__init__.pyc has changed

diff -r 000000000000 -r f493979f1408 util/add_datatype.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/add_datatype.py Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,74 @@
+#!/usr/bin/python
+
+"""
+This script copy the huba datatype into your galaxy:
+    - Add under <registration>, the datatype_conf
+    - Add huba.xml under display_application/ucsc/
+    - Add hubAssembly.py inside lib/galaxy/datatypes
+Place yourself in the folder of the python script, and launch it
+- Based on the fact datatypes_conf
+"""
+
+import argparse
+import os
+import shutil
+import sys
+import xml.etree.ElementTree as ET
+
+
+def main(argv):
+    # Command Line parsing init
+    parser = argparse.ArgumentParser(description='Create a foo.txt inside the given folder.')
+
+    parser.add_argument('-g', '--galaxy_root', help='Galaxy root folder', required=True)
+
+    # Get the args passed in parameter
+    args = parser.parse_args()
+
+    galaxy_root_path = args.galaxy_root
+
+    add_datatype_conf(galaxy_root_path)
+    add_huba_xml(galaxy_root_path)
+    add_hubAssembly(galaxy_root_path)
+
+
+def add_datatype_conf(galaxy_root_path):
+    print "======= Add datatype ======="
+    datatype_conf_path = os.path.join(galaxy_root_path, 'config/datatypes_conf.xml')
+    # TODO: Not relative to this python file but based on a parameter galaxy_root
+    # TODO: Check if datatypes_conf.xml, if not create it by copying datatypes_conf.xml.sample
+    # TODO: For debug only
+    # tree = ET.parse('../test-data/add_datatype/datatypes_conf.xml.sample')
+    # TODO: UnComment for prod
+    tree = ET.parse(datatype_conf_path)
+    root = tree.getroot()
+    print root.tag
+    registration = root[0]
+    print registration.attrib
+
+    huba_datatype = ET.parse('../trackHub/datatypes_conf.xml').getroot()
+    # TODO: Verify the datatype is not already existing, else do not add / write. And in another version, check it
+    registration.append(huba_datatype)
+    tree.write(datatype_conf_path)
+    print "datatype added in %s" % datatype_conf_path
+    return
+
+
+def add_huba_xml(galaxy_root_path):
+    print "======= Add hub xml ======="
+    displayApp_ucsc_path = os.path.join(galaxy_root_path, "display_applications/ucsc/")
+    shutil.copy("../trackHub/huba.xml", displayApp_ucsc_path)
+    print "Content of %s now: %s" % (displayApp_ucsc_path, os.listdir(displayApp_ucsc_path))
+    return
+
+
+def add_hubAssembly(galaxy_root_path):
+    print "======= Add hubAssembly ======="
+    datatype_lib_path = os.path.join(galaxy_root_path, "lib/galaxy/datatypes/")
+    shutil.copy("../trackHub/hubAssembly.py", datatype_lib_path)
+    print "Content of %s now: %s" % (datatype_lib_path, os.listdir(datatype_lib_path))
+    return
+
+
+if __name__ == "__main__":
+    main(sys.argv)

diff -r 000000000000 -r f493979f1408 util/cleanDirectory.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/cleanDirectory.py Wed Dec 21 12:13:04 2016 -0500

@@ -0,0 +1,14 @@
+#!/usr/bin/python
+"""Use to clean the directory after the run of HubArchiveCreator.py manually"""
+import os
+import shutil
+
+# Remove 'myHub.zip at root folder
+try:
+    os.remove('myHub.zip')
+except OSError as o:
+    # We don't need to crash the program
+    print 'Warning: ' + str(o)
+
+# Remove 'myHub' folder and its content
+shutil.rmtree('myHub', ignore_errors=True)

diff -r 000000000000 -r f493979f1408 util/install_linux_binaries
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/install_linux_binaries Wed Dec 21 12:13:04 2016 -0500

[

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+localBinPath="/usr/local/bin/"
+hgDownloadURl="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/"
+
+# Binaries needed for HAC
+twoBitInfo="twoBitInfo"
+faToTwoBit="faToTwoBit"
+gff3ToGenePred="gff3ToGenePred"
+gtfToGenePred="gtfToGenePred"
+genePredToBed="genePredToBed"
+# sort="sort"
+bedToBigBed="bedToBigBed"
+
+binariesArray=( ${twoBitInfo} ${faToTwoBit} ${gff3ToGenePred} ${gtfToGenePred} ${genePredToBed} ${bedToBigBed} )
+
+# Download and install binaries
+for binaryName in "${binariesArray[@]}"
+do
+    binaryInstallationPath="${localBinPath}/${binaryName}"
+    sudo wget -P ${localBinPath} "${hgDownloadURl}/${binaryName}"
+    sudo chown ${USER} ${binaryInstallationPath}
+    sudo chmod +x ${binaryInstallationPath}
+done

diff -r 000000000000 -r f493979f1408 util/subtools.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/util/subtools.py Wed Dec 21 12:13:04 2016 -0500

[

b'@@ -0,0 +1,245 @@\n+#!/usr/bin/python\n+# -*- coding: utf8 -*-\n+\n+"""\n+This class handles the subprocess calls of the different tools used\n+in HubArchiveCreator\n+"""\n+\n+import logging\n+import os\n+import subprocess\n+import sys\n+\n+class PopenError(Exception):\n+ def __init__(self, cmd, error, return_code):\n+ self.cmd = cmd\n+ self.error = error\n+ self.return_code = return_code\n+\n+ def __str__(self):\n+ message = "The subprocess {0} has returned the error: {1}.".format(self.cmd, self.return_code)\n+ message = \',\'.join((message, "Its error message is: {0}".format(self.error)))\n+ return repr(message)\n+\n+def _handleExceptionAndCheckCall(array_call, **kwargs):\n+ """\n+ This class handle exceptions and call the tool.\n+ It maps the signature of subprocess.check_call:\n+ See https://docs.python.org/2/library/subprocess.html#subprocess.check_call\n+ """\n+ stdout = kwargs.get(\'stdout\', subprocess.PIPE)\n+ stderr = kwargs.get(\'stderr\', subprocess.PIPE)\n+ shell = kwargs.get(\'shell\', False)\n+\n+ cmd = array_call[0]\n+\n+ output = None\n+ error = None\n+\n+ # TODO: Check the value of array_call and <=[0]\n+ logging.debug("Calling {0}:".format(cmd))\n+\n+ logging.debug("---------")\n+\n+ # TODO: Use universal_newlines option from Popen?\n+ try:\n+ p = subprocess.Popen(array_call, stdout=stdout, stderr=stderr, shell=shell)\n+\n+ # TODO: Change this because of possible memory issues => https://docs.python.org/2/library/subprocess.html#subprocess.Popen.communicate\n+\n+ output, error = p.communicate()\n+\n+ if stdout == subprocess.PIPE:\n+ logging.debug("\\t{0}".format(output))\n+ else:\n+ logging.debug("\\tOutput in file {0}".format(stdout.name))\n+ # If we detect an error from the subprocess, then we raise an exception\n+ # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process\n+ # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.\n+ if p.returncode:\n+ if stderr == subprocess.PIPE:\n+ raise PopenError(cmd, error, p.returncode)\n+ else:\n+ # TODO: To Handle properly with a design behind, if we received a option as a file for the error\n+ raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"\\\n+ .format(cmd, stderr.name, p.returncode))\n+\n+ except OSError as e:\n+ message = "The subprocess {0} has encountered an OSError: {1}".format(cmd, e.strerror)\n+ if e.filename:\n+ message = \'\\n\'.join((message, ", against this file: {0}".format(e.filename)))\n+ logging.error(message)\n+ sys.exit(-1)\n+ except PopenError as p:\n+ message = "The subprocess {0} has returned the error: {1}.".format(p.cmd, p.return_code)\n+ message = \'\\n\'.join((message, "Its error message is: {0}".format(p.error)))\n+\n+ logging.exception(message)\n+\n+ sys.exit(p.return_code)\n+ except Exception as e:\n+ message = "The subprocess {0} has encountered an unknown error: {1}".format(cmd, e)\n+ logging.exception(message)\n+\n+ sys.exit(-1)\n+ return p\n+\n+def twoBitInfo(two_bit_file_name, two_bit_info_file):\n+ """\n+ Call twoBitInfo and write the result into twoBit_info_file\n+ :param two_bit_file_name:\n+ :param two_bit_info_file:\n+ :return the subprocess.check_call return object:\n+ """\n+ array_call = [\'twoBitInfo\', two_bit_file_name, two_bit_info_file]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def faToTwoBit(fasta_file_name, twoBitFile):\n+ """\n+ This function call faToTwoBit UCSC tool, and return the twoBitFile\n+ :param fasta_file_name:\n+ :param mySpecieFolder:\n+ :return:\n+ """\n+\n+ array_call = [\'faToTwoBit\', fasta_file_name, twoBitFile]\n+ _handleExceptionAndCheckCall(array_call)'..b'red_file_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def genePredToBed(gene_pred_file_name, unsorted_bed_file_name):\n+ """\n+ Call genePredToBed and write the result into unsorted_bed_file_name\n+ :param gene_pred_file_name:\n+ :param unsorted_bed_file_name:\n+ :return:\n+ """\n+ array_call = [\'genePredToBed\', gene_pred_file_name, unsorted_bed_file_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def sort(unsorted_bed_file_name, sorted_bed_file_name):\n+ """\n+ Call sort with -k1,1 -k2,2n on unsorted_bed_file_name and write the result into sorted_bed_file_name\n+ :param unsorted_bed_file_name:\n+ :param sorted_bed_file_name:\n+ :return:\n+ """\n+ array_call = [\'sort\', \'-k\', \'1,1\', \'-k\', \'2,2n\', unsorted_bed_file_name, \'-o\', sorted_bed_file_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):\n+ """\n+ Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name\n+ :param two_bit_info_file_name:\n+ :param chrom_sizes_file_name:\n+ :return:\n+ """\n+ array_call = [\'sort\', \'-k2rn\', two_bit_info_file_name, \'-o\', chrom_sizes_file_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def bedToBigBed(sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name,\n+ typeOption=None, autoSql=None, tab=False):\n+ """\n+ Call bedToBigBed on sorted_bed_file_name, using chrom_sizes_file_name and write the result into big_bed_file_name\n+ :param sorted_bed_file_name:\n+ :param chrom_sizes_file_name:\n+ :param big_bed_file_name:\n+ :return:\n+ """\n+\n+ # TODO: Move this into the _handleExceptionAndCheckCall function\n+ # Parse the array\n+ logging.debug("sorted_bed_file_name: {0}".format(sorted_bed_file_name))\n+ logging.debug("chrom_sizes_file_name: {0}".format(chrom_sizes_file_name))\n+ logging.debug("big_bed_file_name: {0}".format(big_bed_file_name))\n+ logging.debug("typeOption: {0}".format(typeOption))\n+ logging.debug("autoSql: {0}".format(autoSql))\n+ logging.debug("tab option: {0}".format(tab))\n+\n+ array_call = [\'bedToBigBed\', sorted_bed_file_name, chrom_sizes_file_name, big_bed_file_name]\n+ if typeOption:\n+ typeOption = \'\'.join([\'-type=\', typeOption])\n+ array_call.append(typeOption)\n+ if autoSql:\n+ autoSql = \'\'.join([\'-as=\', autoSql])\n+ array_call.append(autoSql)\n+ if tab:\n+ array_call.append(\'-tab\')\n+\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def sortBam(input_bam_file_name, output_sorted_bam_name):\n+ """\n+ Call samtools on input_bam_file_name and output the result in output_sorted_bam_name\n+ :param input_bam_file_name:\n+ :param output_sorted_bam_name:\n+ :return:\n+ """\n+ array_call = [\'samtools\', \'sort\', input_bam_file_name, \'-o\', output_sorted_bam_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def createBamIndex(input_sorted_bam_file_name, output_name_index_name):\n+ """\n+ Call `samtools index` on imput_sorted_bam_file_name and output the result in output_name_index_name\n+ :param input_sorted_bam_file_name:\n+ :param output_name_index_name:\n+ :return:\n+ """\n+ array_call = [\'samtools\', \'index\', input_sorted_bam_file_name, output_name_index_name]\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n+\n+def pslToBigPsl(input_psl_file_name, output_bed12_file_name):\n+ """\n+ Call `pslToBigPsl` on input_psl_file_name and output the result in output_bed12_file_name\n+ :param input_psl_file_name: Name of the psl input file\n+ :param output_bed12_file_name: Name of the output file where to store the result of the cmd\n+ :return:\n+ """\n+ # The command to send\n+ array_call = [\'pslToBigPsl\', input_psl_file_name, output_bed12_file_name]\n+\n+ p = _handleExceptionAndCheckCall(array_call)\n+ return p\n'

diff -r 000000000000 -r f493979f1408 util/subtools.pyc

Binary file util/subtools.pyc has changed