Have implicit SAM to BAM converter sort the output BAM file so that indexing will not fail.

lib/galaxy/datatypes/converters/sam_to_bam.py

@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for converting SAM to BAM, with sorting.
+%prog input_filename.sam output_filename.bam
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    (options, args) = parser.parse_args()
+    
+    assert len( args ) == 2, 'You must specify the input and output filenames'
+    input_filename, output_filename = args
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-sam_to_bam_converter-' )
+    
+    #convert to SAM
+    unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
+    unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
+    cmd = 'samtools view -bS "%s" > "%s"' % ( input_filename, unsorted_bam_filename )
+    proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr = open( unsorted_stderr_filename )
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    #sort sam, so indexing will not fail
+    sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
+    sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
+    cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_filename )
+    proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr = open( sorted_stderr_filename )
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()

lib/galaxy/datatypes/converters/sam_to_bam.xml

@@ -1,11 +1,11 @@
-<tool id="CONVERTER_sam_to_bam" name="Convert SAM to BAM" version="1.0.0">
+<tool id="CONVERTER_sam_to_bam" name="Convert SAM to BAM" version="2.0.0">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <!-- FIXME: conversion will only work if headers for reference sequences are in input file.
          To fix this: (a) merge sam_to_bam tool in tools with this conversion (like fasta_to_len 
          conversion); and (b) define a datatype-specific way to set converter parameters.
       -->
-    <command>samtools view -bS $input1 > $output 2> /dev/null </command>
+    <command interpreter="python">sam_to_bam.py $input1 $output</command>
     <inputs>
         <param name="input1" type="data" format="sam" label="SAM file"/>
     </inputs>