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Consume stderr

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E Rasche
2017-09-25 11:39:14 +02:00
parent b326130984
commit 8f4491bfff
1 changed files with 2 additions and 2 deletions
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lib/galaxy/datatypes/binary.py
+2 -2
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@@ -254,7 +254,7 @@ class Bam(Binary):
# Get the version of samtools via --version-only, if available
try:
output = subprocess.check_output(['samtools', '--version-only'])
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]
@@ -263,7 +263,7 @@ class Bam(Binary):
# --version-only not available
pass
output = subprocess.check_output(['samtools'])
output = subprocess.check_output(['samtools'], stderr=subprocess.PIPE)
lines = output.split('\n')
for line in lines:
if line.lower().startswith('version'):