Proposal: Make microViz available via Bioconda (and/or Bioconductor)

[fmerinocasallo]

Hi @david-barnett! 👋

microViz has been very useful for Principal Coordinates Analysis (PCoA) as part of our metatranscriptomics workflows. Installing microViz would be even smoother if it were available through a conda channel. I've been working on conda recipes (most recently for r-khroma) and wanted to share a path forward tailored to microViz.

I noticed that while microViz is available in a private Anaconda channel (CGR-lab), it's not yet available in the official Bioconda or conda-forge repositories. Since microViz depends heavily on Bioconductor packages (phyloseq, microbiome, ComplexHeatmap, etc.) that are already well-maintained in Bioconda, I thought it would make sense to have microViz available there as well.

I've prepared a draft Bioconda recipe for microViz as a starting point. I wanted to reach out to see if you'd be interested in submitting it yourself.

Note that contributing a package to Bioconda makes you the maintainer of that package.

I've attached draft recipe files to this issue (meta.yaml, build.sh, and bld.bat) as a first approximation:

meta.yaml
build.sh

Since GitHub doesn't allow me to upload the bld.bat, this would be its content:

"%R%" CMD INSTALL --build . %R_ARGS%
IF %ERRORLEVEL% NEQ 0 exit /B 1

These should be reviewed and validated before submission to ensure everything is correct.

Why Bioconda/conda matters for microViz

• Dependencies already shipped: Key Bioconductor dependencies such as phyloseq, microbiome, ComplexHeatmap, vegan, etc., are already packaged in Bioconda (e.g., bioconductor-phyloseq is at 1.50.0 with >250k downloads). Users could therefore install microViz plus its full dependency stack via one conda install command.

• Minimal friction for Bioconductor-based stacks: Bioconda's contributor workflow mirrors conda-forge's staged-recipes but is tuned for Bioconductor software. The contributor guide and tutorials walk through recipe authoring, optional build scripts, local testing, and PR review/linting (links listed below).

• ARM builds ready: Bioconda now offers opt-in linux-aarch64 and osx-arm64 builds by adding:

  extra:
    additional-platforms:
      - linux-aarch64
      - osx-arm64
  

  to the recipe, enabling Apple Silicon and ARM server support. Note that if you enable ARM builds, you may need to update the build.sh file to include these platforms in the if clause.

Bioconductor as a complementary (or primary) route

Because microViz already leans heavily on Bioconductor packages, submitting it directly to Bioconductor might also be attractive. Their contribution guides cover the GitHub-issue submission, R CMD check expectations, git workflow, and reviewer milestones (links listed below). If microViz enters Bioconductor, it will automatically flow into Bioconda packages afterward.

Documentation and Resources

If you're interested in the Bioconda route, here are some helpful links:

• Contributing packages to Bioconda: https://bioconda.github.io/contributor/index.html
• Bioconda tutorials: https://bioconda.github.io/tutorials/index.html
• ARM builds (optional): https://bioconda.github.io/developer/aarch64.html
• Bioconda recipes repository: https://github.com/bioconda/bioconda-recipes (where recipes are submitted)

Conversely, if you prefer the Bioconductor route, here are some useful links:

• Bioconductor Contributions repo: https://github.com/Bioconductor/Contributions
• Bioconductor submission guide: https://contributions.bioconductor.org/bioconductor-package-submissions.html
• Bioconductor developer overview: https://contributions.bioconductor.org/develop-overview.html
• Bioconductor git workflow: https://contributions.bioconductor.org/git-version-control.html#new-package-workflow
• PKG review docs: https://github.com/Bioconductor/pkgrevdocs

What's Involved

As a Bioconda maintainer, you would be responsible for:

• Updating the recipe when new versions are released (usually straightforward - just version number and SHA256)
• Responding to occasional issues in the feedstock repository
• Ensuring the package continues to build correctly (Bioconda CI handles most of this automatically)

I'm happy to help with the submission process if needed.

Thanks again for microViz! 💙

Best regards,
Fran

[david-barnett]

Hi Fran, thanks for your interest in microViz 🙂

I would likely go the bioconductor (or cran) submission route. This is easier said than done though, as microViz has a bunch of dependencies that frequently update, and currently also a few failing tests and legacy code issues I'd need to iron out before a submission. Based on my current schedule I'll have to come back to this idea in February at earliest I'm afraid.

Alternatively/in the meantime you could perhaps incorporate the docker image (or via singularity) into your workflows.

best,
David