From 43159db9fef7d2d14586d5bf8946f4a79e5f2062 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 28 Jan 2015 13:25:11 -0500 Subject: [PATCH] Use subprocess.call() rather than Popen(), thanks Nicola. --- lib/galaxy/datatypes/binary.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 9d4129c464b..4fe54baabff 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -275,8 +275,7 @@ class Bam( Binary ): 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() + 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)