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Use a symlink to the dataset in the same directory as the MetadataTempFile as the input to samtools index so there's no clobber risk. Thanks Dan.

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This commit is contained in:
Nate Coraor
2015-01-28 11:58:23 -05:00
parent 13e8b3e7de
commit 11ae48a70f
1 changed files with 12 additions and 7 deletions
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lib/galaxy/datatypes/binary.py
+12 -7
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@@ -270,13 +270,18 @@ class Bam( Binary ):
#Did index succeed?
if exit_code == -6:
# SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter.
command = [ 'samtools', 'index', dataset.file_name ]
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
if os.path.exists( os.path.join( dataset.file_name, '.bai' ) ):
shutil.move( os.path.join( dataset.file_name, '.bai' ), index_file.file_name )
else:
open( stderr_name, 'ab+' ).write( 'Galaxy attempted to build the BAM index with samtools 1.0+ but failed\n')
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 ]
proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
exit_code = proc.wait()
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: