Temporary folder for cache building singularity containers at HPC

[maartenpaul]

When pulling containers, normally singularity is using the /tmp folder for storing the cache. For large containers the /tmp is too small and hence building the container via biomero is not working. It is recommended to

It is recommended to set the singularity/apptainer cache to the scratch

export SCRATCH = /scratchdata/$USER export APPTAINER_TMPDIR=$SCRATCH/.apptainer-tmp export APPTAINER_CACHEDIR=$SCRATCH/.apptainer-cache mkdir -p $APPTAINER_TMPDIR mkdir -p $APPTAINER_CACHEDIR

See here: https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/103809025/Apptainer+Singularity+containers#Temporary-files

Is there a way to set this cache dirs in biomero or should I just add this to e.g. my ~/.bashrc . In that case it might be useful to mention this in the documentation.

[TorecLuik]

It's on the backlog (#48) to allow changing the building folder via BIOMERO configuration.

In the meantime, I guess some manual env var setting if that works yes. Just note that a "headless SSH session" doesn't always use the same startup files as a manual SSH session.