# HG changeset patch
# User matt-shirley
# Date 1380157335 14400
# Node ID da2dbe22f80b05f916bfbdb5d2865f390ce2c0af
# Parent c386fe82db82609a64ec075ba79f51bef715876d
Deleted selected files
diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/datatypes_conf.xml
--- a/sra_tools-04cc8176e86f/datatypes_conf.xml Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
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diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/fastq_dump.xml
--- a/sra_tools-04cc8176e86f/fastq_dump.xml Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-
- from NCBI SRA.
-
- fastq-dump --log-level fatal
- #if $input.input_select == "file":
- --accession '${input.file.name}'
- #else:
- --accession $input.accession
- #end if
- --defline-seq '@\$sn[_\$rn]/\$ri'
- --stdout
- #if $split == "yes":
- --split-spot
- #end if
- #if str( $alignments ) == "aligned":
- --aligned
- #end if
- #if str( $alignments ) == "unaligned":
- --unaligned
- #end if
- #if str( $minID ) != "":
- --minSpotId $minID
- #end if
- #if str( $maxID ) != "":
- --maxSpotId $maxID
- #end if
- #if str( $minlen ) != "":
- --minReadLen $minlen
- #end if
- #if str( $readfilter ) != "":
- --read-filter $readfilter
- #end if
- #if str( $region ) != "":
- --aligned-region $region
- #end if
- #if str( $spotgroups ) != "":
- --spot-groups $spotgroups
- #end if
- #if str( $matepairDist ) != "":
- --matepair-distance $matepairDist
- #end if
- #if $clip == "yes":
- --clip
- #end if
- #if str( $outputformat ) == "fasta":
- --fasta
- #end if
- #if $input.input_select=="file":
- $input.file
- #else:
- $input.accession
- #end if
- > $output
-
- fastq-dump --version
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- sra_toolkit
-
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- This tool extracts reads from SRA archives using fastq-dump.
- Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
- The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
- Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-
-
diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sam_dump.xml
--- a/sra_tools-04cc8176e86f/sam_dump.xml Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-
- in SAM format from NCBI SRA.
-
- sam-dump --log-level fatal
- #if str( $region ) != "":
- --aligned-region $region
- #end if
- #if str( $matepairDist ) != "":
- --matepair-distance $matepairDist
- #end if
- #if str( $minMapq ) != "":
- --minmapq $minMapq
- #end if
- #if $header == "yes":
- --header
- #else:
- --no-header
- #end if
- #if str( $alignments ) == "both":
- --unaligned
- #end if
- #if str( $alignments ) == "unaligned":
- --unaligned-spots-only
- #end if
- #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
- --primary
- #end if
- #if str( $fastq ) == "yes":
- --fastq
- #end if
- #if $input.input_select == "file":
- $input.file
- #elif $input.input_select == "accession_number":
- $input.accession
- #elif $input.input_select == "text":
- `cat $input.text`
- #end if
- > $output
-
- sam-dump --version
-
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- sra_toolkit
-
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- This tool extracts reads from sra archives using sam-dump.
- Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
- The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
- Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-
-
\ No newline at end of file
diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sra.py
--- a/sra_tools-04cc8176e86f/sra.py Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-"""
-NCBI sra class
-"""
-import logging
-import binascii
-from galaxy.datatypes.data import *
-from galaxy.datatypes.sniff import *
-from galaxy.datatypes.binary import *
-from galaxy.datatypes.metadata import *
-
-log = logging.getLogger(__name__)
-
-class sra( Binary ):
- """ Sequence Read Archive (SRA) """
- file_ext = 'sra'
-
- def __init__( self, **kwd ):
- Binary.__init__( self, **kwd )
- def sniff( self, filename ):
- """ The first 8 bytes of any NCBI sra file is 'NCIB.sra', and the file is binary. EBI and DDBJ files may differ, though EBI and DDBJ
- submissions through NCBI (ERR and DRR accessions) read 'NCBI.sra'.
- For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure
- """
- try:
- header = open(filename).read(8)
- if binascii.b2a_hex(header) == binascii.hexlify('NCBI.sra'):
- return True
- else:
- return False
- except:
- return False
- def set_peek(self, dataset, is_multi_byte=False):
- if not dataset.dataset.purged:
- dataset.peek = 'Binary sra file'
- dataset.blurb = data.nice_size(dataset.get_size())
- else:
- dataset.peek = 'file does not exist'
- dataset.blurb = 'file purged from disk'
- def display_peek(self, dataset):
- try:
- return dataset.peek
- except:
- return 'Binary sra file (%s)' % ( data.nice_size(dataset.get_size()))
-
-if hasattr(Binary, 'register_sniffable_binary_format'):
- Binary.register_sniffable_binary_format('sra', 'sra', sra)
diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/sra_pileup.xml
--- a/sra_tools-04cc8176e86f/sra_pileup.xml Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-
- from NCBI sra.
- sra-pileup --log-level fatal
- #if str( $region ) != "":
- --aligned-region $region
- #end if
- #if str( $minMapq ) != "":
- --minmapq $minMapq
- #end if
- #if $input.input_select == "file":
- $input.file
- #elif $input.input_select == "accession_number":
- $input.accession
- #elif $input.input_select == "text":
- `cat $input.text`
- #end if
- > $output
- sra-pileup --version
-
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- sra_toolkit
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- This tool produces pileup format from sra archives using sra-pileup.
- Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
- The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
- Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-
-
diff -r c386fe82db82 -r da2dbe22f80b sra_tools-04cc8176e86f/tool_dependencies.xml
--- a/sra_tools-04cc8176e86f/tool_dependencies.xml Wed Sep 25 21:00:05 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-
-
-
-
-
- http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.3-3/sra_sdk-2.3.3-3.tar.gz
- make release
- make static
- make
- $INSTALL_DIR/bin
- $INSTALL_DIR/ncbi
- $INSTALL_DIR/ncbi/public
- sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" bin64/ncbi/default.kfg
- cp --recursive --dereference bin64/* $INSTALL_DIR/bin
- $INSTALL_DIR/bin
-
-
- Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
-This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
-When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
-download of a large SRA data set.
-
-Build Requirements:
- ar
- bash
- make
- gcc, g++
- libxml2
- libcurl4
- zlib
-
-On a debian based Linux OS use:
-
- apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
-
-
-