Update the singularity command line parameter for apptainer

[kinow]

Placeholder issue for future work after Singularity has moved to under the Linux Foundation as “Apptainer”.

From @mr-c on Element about renaming --singularity to --apptainer in cwltool:

Sure, but we'll likely keep the other name as a fallback.
Or better yet, auto detect which engine is installed. I believe there is an issue for that already

[salexan2001]

Could you please link the issue for the autodetection of the singularity engine? I am having issues with usage of apptainer together with cwltool and I am looking for more information.

[mr-c]

#642

[tom-tan]

Related issue:

There were two similar but different implementation of "Singularity". That is:

• the original version by Lawrence Berkeley National Laboratory (that is now rebranded to Apptainer), and
• the forked version by Sylabs (the document by Sylabs call it SingularityCE since v3.8).

I know they shared most of the code base but we have to distinguish one to another because they will have different feature set in the future.

I am curious which singularity (or both) is currently supported by cwltool.

[mr-c]

@tom-tan In theory, both should work. Currently the name of the command line interface to apptainer/singularity is hardcoded to singularity; that could be made configurable..

[salexan2001]

However, there seems to be an error regarding the "version check", as apptainer and singularity seem to have different versioning conventions. I am currently receiving the following error with apptainer:

ERROR Workflow error, try again with --debug for more information:
Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: invalid literal for int() with base 10: 'a'

... while it works perfectly with the syslabs-singularity (and also with standard docker in this case).

(I started the job using $ cwltool --singularity 1st-tool.yml echo-job.yml)

So probably either the two command lines (--singularity / --apptainer) need a specific version check or the versioning scheme needs to be auto-detected depending on whether the one or the other singularity distribution is used.

I have attached the (slightly shortened) full output with --debug option:

bug_report_cwltool.txt

[mr-c]

Thank you @salexan2001 for trying this out. Would you be able to help us implement auto-detection of docker / podman / singularity / apptainer with correct version parsing?

[salexan2001]

Sure, I will have a look at the contribution guidelines and prepare a pull request. I have no experience with podman so far.

[mr-c]

@salexan2001 Thanks! I can help with the podman side. I don't think we track the version there, so for podman we only need to use shutil.which() to detect if it is on the system path