annotate srf2fastq/README @ 0:d901c9f41a6a default tip

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

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"/>