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Singularity version extraction breaks with singularity-ce #1545
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Thanks @jmfernandez and @Acivico for your report. Can you share the output of |
Yes, of course! (s) jmfernandez@olympo[30]:/tmp/bb> singularity version
3.8.1
(s) jmfernandez@olympo[31]:/tmp/bb> singularity --version
singularity-ce version 3.8.1 |
mr-c
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Thanks @jmfernandez! Can you confirm the fix in #1547 ? |
Yes, I can confirm you that it is now working with singularity-ce |
mr-c
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Expected Behavior
When singularity-ce is installed following instructions at https://sylabs.io/guides/3.8/user-guide/quick_start.html#download-singularityce-from-a-release) and cwltool is ran in singularity mode, it should work.
Actual Behavior
When singularity-ce is installed and cwltool is ran in singularity mode, an unexpected exception arises. Our undergraduate student @Acivico found it when he was installing in his computer the prerequisites for WfExS-backend.
Workflow Code
As this issue is after workflow parsing but before workflow execution, when Singularity version is being detected, any minimal workflow fires it. For instance:
Full Traceback
cwltool --debug --singularity echo.cwl --message world
Your Environment
Check using
cwltool --version
Additional notes
The bug is at
cwltool/cwltool/singularity.py
Lines 26 to 43 in aec33fc
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