search

martius-lab / cluster_utils

https://cluster-utils.readthedocs.io/stable/
Other
12 stars 0 forks source link

Pass configured environment variables to singularity #92

Closed mseitzer closed 5 months ago

mseitzer commented 6 months ago

Previously, environment variables set in the environment setup were not visible to singularity if running with --cleanenv or --containall.

Also switch order of setting environment variables and pre_job_script to allow the script to use the environment variables (useful to write more generic scripts).

Partially addresses #68.

luator commented 6 months ago

Looks good now, thanks! (sorry for the merge conflict :sweat_smile: )

luator commented 6 months ago

@mseitzer This can be merged right? If you don't have time right now, I can take care of the merge conflicts.