ideas for a new 24.x version

[bgruening]

• get CVMFS in userspace working (https://github.com/galaxyproject/ansible-role-cvmfsexec, https://github.com/galaxyproject/usegalaxy-playbook/blob/6341fbc7d5d0649d00c66dcc10b45d7f16f113a7/env/common/host_vars/vm030.bridges2.psc.edu.yml#L157)
  • mount in Singularity containers
  • install tools without Conda by default

[bgruening]

Check if Galaxy really uses job-handlers. I have seen this in the logs:

Dynamic handlers are configured in Gravity but Galaxy is not configured to assign jobs to handlers dynamically, so these handlers will not handle jobs. Set the job handler assignment method in the Galaxy job configuration to db-skip-locked or db-transaction-isolation to fix this.

[jyotipm29]

Yes, job handlers work. You can find the logs in /home/galaxy/logs/ directory.

[jyotipm29]

• get CVMFS in userspace working (https://github.com/galaxyproject/ansible-role-cvmfsexec, https://github.com/galaxyproject/usegalaxy-playbook/blob/6341fbc7d5d0649d00c66dcc10b45d7f16f113a7/env/common/host_vars/vm030.bridges2.psc.edu.yml#L157)

  • mount in Singularity containers
  • install tools without Conda by default
• install conda from conda-forge, miniforge
• investigate muti-stage builds for smaller containers

cvmfsexec does not support Ubuntu currently as stated here.

[bgruening]

What a bummer, ok for now let's assume we run with --privileged

[bgruening]

• mention dive https://github.com/wagoodman/dive in our Readme, to assist in finding large data that we can remove

[bgruening]

• we could also integrate dive into our CI testing: https://github.com/wagoodman/dive?tab=readme-ov-file#ci-integration

[bgruening]

mount in the singularity containers:

cvmfs2 /cvmfs/singularity.galaxyproject.org fuse ro,nosuid,nodev,relatime,user_id=0,group_id=0,default_permissions,allow_other 0 0