Closed jmfernandez closed 2 years ago
Thanks @jmfernandez and @Acivico for your report. Can you share the output of singularity version
with singularity-ce?
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
Thanks @jmfernandez! Can you confirm the fix in https://github.com/common-workflow-language/cwltool/pull/1547 ?
Yes, I can confirm you that it is now working with singularity-ce
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
cwltool --version
Additional notes
The bug is at https://github.com/common-workflow-language/cwltool/blob/aec33fcfa3459a90cbba8c88ebb991be94d21429/cwltool/singularity.py#L26-L43 , where the singularity version extraction is too rigid