integration of RE Galaxy #210
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martenson
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Jul 16, 2025
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galaxy-re VM didn't have a privileged user (e.g., debian) so we need to create one manually |
martenson
reviewed
Dec 16, 2025
| LC_ALL: C | ||
| # The cache directory holds the docker containers that get converted | ||
| SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/" | ||
| SINGULARITY_CACHEDIR: "{{ galaxy_mutable_data_dir }}/singularity/cache" |
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martenson
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Dec 17, 2025
| opts: rw,_netdev | ||
| state: mounted | ||
| - name: Create galaxy mutable data directory | ||
| - name: Create RBD data directory |
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A note about what is RBD used for and how we treat it (maybe in a readme?) would be welcome
martenson
reviewed
Dec 17, 2025
group_vars/galaxyservers.yml
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| galaxy_commit_id: release_25.0 | ||
| galaxy_force_checkout: true | ||
| galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml" | ||
| galaxy_data_dir: "{{ galaxy_mutable_data_dir }}" |
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I am not sure about this var, if this is truly just some local helper it would be better to not have the galaxy_ prefix, because it is not related to the galaxy role.
martenson
reviewed
Dec 17, 2025
… points because one is only on Galaxy site (/data/.../tool_data)
martenson
reviewed
Jan 8, 2026
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I just ran it on REgalaxy, and it works. Only GCZ remains. I think we are ready to merge |
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