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Merged in natefoo/galaxy-central/samtools1_bam_index (pull request #651)

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Allow BAM's set_meta() to use samtools 1 to generate the index, if the samtools found on $PATH is samtools 1.
This commit is contained in:
Nate Coraor
2015-01-28 13:36:35 -05:00
parent bff841fa42 43159db9fe
commit e7bfac8046
1 changed files with 15 additions and 2 deletions
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lib/galaxy/datatypes/binary.py
+15 -2
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@@ -264,10 +264,23 @@ class Bam( Binary ):
##$ samtools index
##Usage: samtools index <in.bam> [<out.index>]
stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name )
proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
command = [ 'samtools', 'index', dataset.file_name, index_file.file_name ]
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
#Did index succeed?
if exit_code == -6:
# SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter.
dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ),
'__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) )
os.symlink( dataset.file_name, dataset_symlink )
try:
command = [ 'samtools', 'index', dataset_symlink ]
exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
shutil.move( dataset_symlink + '.bai', index_file.file_name )
except Exception, e:
open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed: %s\n' % e)
finally:
os.unlink( dataset_symlink )
stderr = open( stderr_name ).read().strip()
if stderr:
if exit_code != 0: