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usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
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Problems with Apptainer environment variables #84

Closed kjetilkl closed 1 year ago

kjetilkl commented 1 year ago

After resuming the ecc1 and ecc2 nodes - which now run the new "apptainer" instead of the old "singularity" - several tools fail simply because the following text is written to STDERR and Galaxy assumes this indicates an error:

DEPRECATED USAGE: Environment variable SINGULARITY_TMPDIR will not be supported in the future, use APPTAINER_TMPDIR instead
kjetilkl commented 1 year ago

Solution:

I added the following environment variables alongside SINGULARITY_CACHEDIR and SINGULARITY_TMPDIR to the file /srv/galaxy/dynamic_rules/usegalaxy/destination_specifications.yaml (in two places).

APPTAINER_CACHEDIR: /var/tmp/containers
APPTAINER_TMPDIR: /var/tmp

That stopped Singularity/Apptainer from complaining.