Bioconductor on conda

Install

$ conda create -n bioc bioconductor-deseq2 \
    --override-channels --strict-channel-priority \
    -c https://conda.biocpkgcontainers.org -c conda-forge

$ mamba create -n bioc bioconductor-deseq2 \
    --override-channels --strict-channel-priority \
    -c https://conda.biocpkgcontainers.org -c conda-forge

$ pixi init --channel https://conda.biocpkgcontainers.org --channel conda-forge
$ pixi add bioconductor-deseq2

# ~/.condarc with Miniforge, which has no defaults channel
channels:
  - https://conda.biocpkgcontainers.org
  - conda-forge
channel_priority: strict

• Channel orderList this channel before conda-forge, with strict priority. Do not mix it with bioconda.
• No Anaconda licenseNothing here uses conda's defaults channel, which needs a paid license at large organizations. --override-channels keeps conda off it, and Miniforge, micromamba and pixi do not configure it.
• Package namesbioconductor- plus the package name in lowercase, such as bioconductor-deseq2.
• CRAN dependenciesconda-forge has no R 4.6 builds yet, so the CRAN packages Bioconductor needs are built here as r-<name>.

Packages