Pass configured environment variables to singularity #92
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luator
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luator
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Looks good now, thanks! (sorry for the merge conflict 😅 ) |
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@mseitzer This can be merged right? If you don't have time right now, I can take care of the merge conflicts. |
Previously, environment variables were not visible to singularity if running with --contain. 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). Note: the pre_job_script is now also run within the virtual environment, if one is configured.
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Previously, environment variables set in the environment setup were not visible to singularity if running with
--cleanenvor--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.