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This commit is contained in:
E Rasche
2017-09-25 11:39:14 +02:00
parent 8f4491bfff
commit 0f7dd52988
1 changed files with 8 additions and 9 deletions
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lib/galaxy/datatypes/converters/sam_to_bam.py
+8 -9
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@@ -34,18 +34,17 @@ def _get_samtools_version():
if not cmd_exists('samtools'):
raise Exception('This tool needs samtools, but it is not on PATH.')
# Get the version of samtools via --version-only, if available
p = subprocess.Popen(['samtools', '--version-only'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
output, error = p.communicate()
# --version-only is available
# Format is <version x.y.z>+htslib-<a.b.c>
if p.returncode == 0:
try:
output = subprocess.check_output(['samtools', '--version-only'], stderr=subprocess.PIPE)
# --version-only is available
# Format is <version x.y.z>+htslib-<a.b.c>
version = output.split('+')[0]
return version
except subprocess.CalledProcessError:
# --version-only not available
pass
output = subprocess.Popen(['samtools'], stderr=subprocess.PIPE, stdout=subprocess.PIPE).communicate()[1]
output = subprocess.check_output(['samtools'], stderr=subprocess.PIPE)
lines = output.split('\n')
for line in lines:
if line.lower().startswith('version'):