Bioinformatics SIG Proposal

Project Discussion
1

Hi!

I’m a Fedora maintainer and bioinformatics researcher, and I’d like to gauge interest in creating a Bioinformatics SIG dedicated to packaging and maintaining bioinformatics and computational biology tools in Fedora.

The Gap

Right now, researchers who use Fedora for bioinformatics work face a fragmented landscape:

  • Core tools like BLAST, SAMtools, Bowtie2, HMMER, BWA, and BEDTools have no robust RPM packages in the official repos.
  • Biopython exists, but most of the ecosystem is missing.
  • The Medical SIG lists bioinformatics in its scope, but is (understandably) focused on broader medical practice and imaging.
  • The SciTech SIG has a Bioinformatics Wish List, but it hasn’t seen much activity.
  • In practice, most of us end up relying on Bioconda or building from source, which works, but means Fedora is not a main choice for this domain.

What This SIG Would Do

Short-term goals:

  • Identify and prioritize the most-needed bioinformatics tools for RPM packaging
  • Start packaging core tools (sequence alignment, variant calling, phylogenetics, structural biology)
  • Set up a COPR repository for early builds and community testing
  • Coordinate with the Medical SIG, SciTech SIG, and NeuroFedora to avoid duplication

Medium-term goals:

  • Build a Fedora Lab (or Spin) for bioinformatics, a ready-to-use environment for researchers
  • Establish packaging guidelines for bioinformatics software (many tools have complex dependency chains, bundled libraries, or unusual build systems)
  • Create documentation and quickstart guides for researchers on Fedora

Long-term vision:

  • Make Fedora a competitive platform for bioinformatics research, on par with Debian Med
  • Engage with upstream projects to improve build system compatibility with RPM packaging

Who Is This For?

  • Bioinformatics researchers and students who use (or want to use) Fedora
  • Fedora packagers interested in scientific software
  • Anyone working in genomics, proteomics, structural biology, systems biology, or computational biology

What I’m Looking For

  • Are you interested? Even a “+1” or “I’d use this” helps gauge demand.
  • Would you contribute? Packaging, testing, documentation, or just feedback. All welcome!
  • What tools do you need most? What are the first packages you’d want to see?
  • Are there existing efforts I should connect with? I’m aware of the SciTech wish list and Medical SIG, but I may be missing other work.

If there’s enough interest, I’ll set up a wiki page, a Matrix channel, and we can start from there.

Looking forward to hearing from you!

3 Likes
2

Sounds great. +1

Pasting reply from the -devel list

https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/message/EYGL7EMDAZV5UQIC6FF6RKJBQ4FREPTL/

We have the NeuroFedora SIG which does package some computational biology software, but mostly ones that are related to computational neuroscience. Happy to help with/collaborate on neuro related bits.

We’re currently at ~400 packages (!)

Of late, we’ve been reducing the number of packages we maintain because:

  • there’s a lot of software, and the few of us can’t keep up, so we need to (ruthlessly) prioritise
  • for lots of packages, like python packages, we don’t have any evidence to suggest that researchers prefer system packages over installing directly from pypi in virtualenvs—indeed virtualenvs seem to be the norm from anecdotal evidence

We had a comp-neuro lab image that we discontinued for similar reasons.

Our focus is now on packages that are non-trivial to build/compile for users. For Python packages, unless they are necessary to package, we have some regular tests to see if they can be installed off pypi, and we note these in our docs and report upstream: