details: http://www.bx.psu.edu/hg/galaxy/rev/f9bd28601cba changeset: 3007:f9bd28601cba user: Kelly Vincent <kpvincent@bx.psu.edu> date: Tue Nov 10 17:09:02 2009 -0500 description: Changes system call method from subprocess.check_call to os.system in Bam set_meta in images.py. Change to sam_to_bam_out1.bam should fix sam-to-bam functional test. diffstat: lib/galaxy/datatypes/images.py | 12 ++++++------ test-data/sam_to_bam_out1.bam | 2 files changed, 6 insertions(+), 6 deletions(-) diffs (24 lines): diff -r 4fdf952e413e -r f9bd28601cba lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py Tue Nov 10 16:49:05 2009 -0500 +++ b/lib/galaxy/datatypes/images.py Tue Nov 10 17:09:02 2009 -0500 @@ -254,12 +254,12 @@ tmpf1 = tempfile.NamedTemporaryFile(dir=tmp_dir) tmpf1bai = '%s.bai' % tmpf1.name try: - subprocess.check_call(['cd', tmp_dir], shell=True) - subprocess.check_call('cp %s %s' % (dataset.file_name, tmpf1.name), shell=True) - subprocess.check_call('samtools index %s' % tmpf1.name, shell=True) - subprocess.check_call('cp %s %s' % (tmpf1bai, index_file.file_name), shell=True) - except subprocess.CalledProcessError: - sys.stderr.write('There was a problem creating the index for the BAM file\n') + os.system('cd %s' % tmp_dir) + os.system('cp %s %s' % (dataset.file_name, tmpf1.name)) + os.system('samtools index %s' % tmpf1.name) + os.system('cp %s %s' % (tmpf1bai, index_file.file_name)) + except Exception, ex: + sys.stderr.write('There was a problem creating the index for the BAM file\n%s\n' + str(ex)) tmpf1.close() if os.path.exists(tmpf1bai): os.remove(tmpf1bai) diff -r 4fdf952e413e -r f9bd28601cba test-data/sam_to_bam_out1.bam Binary file test-data/sam_to_bam_out1.bam has changed