Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Container variants with different BSgenomes #53997

Open
mfansler opened this issue Feb 20, 2025 · 0 comments
Open

Container variants with different BSgenomes #53997

mfansler opened this issue Feb 20, 2025 · 0 comments
Labels

Comments

@mfansler
Copy link
Member

A user attempting to use the r-archr container encountered issues with the fact that a BSgenome is not preinstalled in the container. Is there precedent for how to best deal with this?

Some options for how we could help with this here:

  1. Naively include a bunch of BSgenomes in the run requirements so they get installed in container.
  2. Build variants with different genomes.
  3. Generate metapackage outputs that have different genomes in the run requirements.

I think (1) undermines users who want to run with minimal footprints. (2) and (3) would only differ by whether end-users are specifying a different package name (or container name) or specifying a build variant string.

Any thoughts about these approaches?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant