bcftools install

[abretaud]

While working on https://github.com/galaxyproject/ansible-galaxy-extras/pull/224 I've notice this little problem:

• start a new 18.09 galaxy container (all-in-one image)
• don't run any tool, or do anything
• run a script to load multiple files into a data library
• I get 4 conda processes trying to install bcftools 1.5 at the same time, all of them failing, and retrying continuously.

I guess it's because the bcftools is required by the set_metadata tool, and it's not installed by default in the docker image. I thought conda was able to have some lock to avoid this kind of simultaneous installs?

I could just install the bcftools env in startup.sh, or in the Dockerfile? Maybe use bioblend to install the dependency, or just make a conda install? Any thoughts on that?

[mvdbeek]

Old Conda versions were attempting to lock, but that didn't work well and was removed. This is why I would not recommend conda_auto_install in production, you'll have the same problem with any other tool that launches simultaneous jobs and requires a dependency that is not installed. I don't think there's an elegant solution yet (we would need a queue to make this work in Galaxy). For your setup I think it'd be OK to just install bcftools in the conda env.

[bgruening]

Thanks to @jyotipm29 we are back on track :smile: The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I would like to close this PR, but please feel free to reopen and rebase against the latest version.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.