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fix: fix singularity logging messages causing conda fail #1523

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merged 3 commits into from Mar 28, 2022
Merged

fix: fix singularity logging messages causing conda fail #1523

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813f85c
fix singularity logging messages causing conda fail
TanguyLallemand Mar 28, 2022
f075589
fix: only use STDOUT for conda version (conda prints version to STDOU…
johanneskoester Mar 28, 2022
5220890
handling stderr on error
johanneskoester Mar 28, 2022
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19 changes: 8 additions & 11 deletions snakemake/deployment/conda.py
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Expand Up @@ -624,19 +624,16 @@ def _check(self):
try:
version = shell.check_output(
self._get_cmd("conda --version"),
stderr=subprocess.STDOUT,
stderr=subprocess.PIPE,
universal_newlines=True,
)
if self.container_img:
version = "\n".join(
filter(
lambda line: not line.startswith("WARNING:")
and not line.startswith("ERROR:"),
version.splitlines(),
)
version_matches = re.findall("\d+.\d+.\d+", version)
if len(version_matches) != 1:
raise WorkflowError(
f"Unable to determine conda version. 'conda --version' returned {version}"
)

version = version.split()[1]
else:
version = version_matches[0]
if StrictVersion(version) < StrictVersion("4.2"):
raise CreateCondaEnvironmentException(
"Conda must be version 4.2 or later, found version {}.".format(
Expand All @@ -645,7 +642,7 @@ def _check(self):
)
except subprocess.CalledProcessError as e:
raise CreateCondaEnvironmentException(
"Unable to check conda version:\n" + e.output.decode()
"Unable to check conda version:\n" + e.stderr.decode()
)

def bin_path(self):
Expand Down