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Fix where singularity build ends up with empty parameter#4

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rpetit3 merged 4 commits into
bactopia:mainfrom
pvanheus:fix_singularity_build_from_docker
May 20, 2026
Merged

Fix where singularity build ends up with empty parameter#4
rpetit3 merged 4 commits into
bactopia:mainfrom
pvanheus:fix_singularity_build_from_docker

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@pvanheus
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The current code yields this command:

ERROR    Command '['singularity', 'build', '',                                           utils.py:57
                             '[PATH]/quay.io-biocontainers-csvtk-0.31.0--h9ee0642_0.img'
                             , 'docker://quay.io/biocontainers/csvtk:0.31.0--h9ee0642_0']' returned non-zero
                             exit status 1.

This PR does two things:

  1. It uses shlex.split rather than string.split to avoid the above-mentioned problem
  2. It produces output event if the command fails (current code raises an exception before producing output)

@rpetit3
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rpetit3 commented May 20, 2026

TYVM @pvanheus

Similar lint/format test fail, I'll fix on my end

@rpetit3 rpetit3 merged commit 3834818 into bactopia:main May 20, 2026
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2 participants