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.