diff srf2fastq/README @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/README	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,94 @@
+This tool comes with io_lib (from Staden package) version 1.12.2
+io_lib is necessary as you will need srf2fastq executable; if you alread have the binary, skip the io_lib installation.
+You may find a more recent version here http://sourceforge.net/projects/staden/files/
+
+1- Install io_lib
+cd io_lib-1.12.2
+./configure --prefix=PREFIX
+make
+make install #assuming you have already superuser permissions granted
+
+2- Edit srf2fastq.sh
+You will need to change the path of srf2fastq executable if
+PREFIX has been defined different from /usr/local:wq
+
+3- Add support for SRF files in galaxy (if galaxy team hasn't added yet)
+Here comes a series of diffs you may want to integrate. lib/galaxy/datatypes/binary.py and lib/galaxy/datatypes/registry.py
+are part of galaxy distribution so a hg diff output is given. datatype_conf.xml is not in
+galaxy repository (the sample is), so a unified diff is given (well, it's the same...)
+
+diff -r 60448575467f lib/galaxy/datatypes/binary.py
+--- a/lib/galaxy/datatypes/binary.py    Mon Aug 23 10:15:17 2010 -0400
++++ b/lib/galaxy/datatypes/binary.py    Wed Aug 25 10:26:38 2010 +0200
+@@ -222,3 +222,31 @@
+         Binary.__init__( self, **kwd )
+         self._magic = 0x8789F2EB
+         self._name = "BigBed"
++
++class Srf( Binary ):
++    """ Illumina Sequence Archive (SRF) """
++    file_ext = "srf"
++
++    def __init__( self, **kwd ):
++        Binary.__init__( self, **kwd )
++    def sniff( self, filename ):
++        try:
++            header = open( filename ).read(4)
++            if binascii.b2a_hex( header ) == binascii.hexlify( 'SSRF' ):
++                return True
++            return False
++        except:
++            return False
++    def set_peek( self, dataset, is_multi_byte=False ):
++        if not dataset.dataset.purged:
++            dataset.peek  = "Binary srf 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 srf file (%s)" % ( data.nice_size( dataset.get_size() ) )
++
+
+diff -r 60448575467f lib/galaxy/datatypes/registry.py
+--- a/lib/galaxy/datatypes/registry.py  Mon Aug 23 10:15:17 2010 -0400
++++ b/lib/galaxy/datatypes/registry.py  Wed Aug 25 10:28:01 2010 +0200
+@@ -173,6 +173,7 @@
+                 'sam'         : tabular.Sam(), 
+                 'scf'         : binary.Scf(),
+                 'sff'         : binary.Sff(),
++                'srf'         : binary.Srf(),
+                 'tabular'     : tabular.Tabular(),
+                 'taxonomy'    : tabular.Taxonomy(),
+                 'txt'         : data.Text(),
+@@ -213,6 +214,7 @@
+         if len(self.sniff_order) < 1:
+             self.sniff_order = [
+                 binary.Bam(),
++                binary.Srf(),
+                 binary.Sff(),
+                 xml.BlastXml(),
+                 sequence.Maf(),
+
+diff -u datatypes_conf.xml datatypes_conf.xml.sample 
+--- datatypes_conf.xml          2010-08-25 10:32:46.778959931 +0200
++++ datatypes_conf.xml.sample   2010-08-25 07:20:34.190956591 +0200
+@@ -105,7 +105,6 @@
+         <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
+         <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/>
+         <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/>
+-        <datatype extension="srf" type="galaxy.datatypes.binary:Srf" mimetype="application/octet-stream" display_in_upload="true"/>
+         <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
+         <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
+         <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+@@ -264,7 +263,6 @@
+           and so on.
+         -->
+         <sniffer type="galaxy.datatypes.binary:Bam"/>
+-        <sniffer type="galaxy.datatypes.binary:Srf"/>
+         <sniffer type="galaxy.datatypes.binary:Sff"/>
+         <sniffer type="galaxy.datatypes.xml:BlastXml"/>
+         <sniffer type="galaxy.datatypes.sequence:Maf"/>