CWL: Problems with path to my python script.

Question

[sibyllewohlgemuth]

Hi! I have python script and a cwl wrapper for the script in the same directory. When I try to run the cwl I get an error because the python script can´t be found. It only works when I specifiy the absolut path to the script in baseCommand. Maybe anyone can give me a hint what I have to add, so the script is found by the cwl-runner? Thanks a lot!

[Devon Ryan]

Have you tried just using the relative path (i.e., ./something.py)?

[sibyllewohlgemuth]

Yes exactly, that is what I tried and what didn´t work. The file is only found when I used the absolute path.

[Devon Ryan]

Not being a CWL person, I assume the working directory is specified somewhere

Answer 1

[Michael R. Crusoe]

Hello sibyllewohlgemuth, thank you for your question.

If your tool isn't wrapped in a container, and it isn't installed on a standard system path, they you'll need to inform your CWL executor where to find it.

Don't forget to chmod a+x my_script.py and ensure that it starts with #!/usr/bin/env python or similar :-)

For example, with the reference implementation, set your PATH and pass in --preserve-environment PATH to cwltool:

PATH=$PATH:/absolute/path/to/the/directory/of/my/script cwltool --preserve-environment PATH my-tool.cwl my-inputs.yaml

If you are using a Docker container with your tool, then this is easy: configure the container to install your script to a standard path like /usr/bin

I hope this was helpful. Cheers,

[sibyllewohlgemuth]

Hi Michael, Thanks a lot for your help! I was missing that I have to set the path and pass it to cwltool! Best, Sibylle

[WouterDeCoster]

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.