conda

A custom conda channel publishing automated pre-release builds of breseq, tracking its master branch.

Channel URL (once published): https://barricklab.github.io/conda/

conda install -c https://barricklab.github.io/conda/ breseq-prerelease

This is not the stable breseq package (that's distributed via bioconda). Packages here are built straight from breseq's master branch and may be broken or unstable; use them to test in-development changes, not for production analysis.

How it works

• recipe/breseq-prerelease/ is a conda-build recipe that builds breseq from a git checkout (source.git_url) rather than a release tarball, and derives a PEP440 dev version from git describe (e.g. 0.40.1.dev42+g3a91c4).
• .github/workflows/build-and-publish.yml runs daily at 7:13 UTC (~3:13am US Eastern) and can also be triggered manually (workflow_dispatch): it checks whether breseq has a new commit since the last publish (scripts/check_new_commit.sh), and if so builds packages for linux-64, linux-aarch64, osx-arm64, and osx-64, and publishes them into the channel (scripts/publish_channel.sh + conda index) hosted on the gh-pages branch.
• state/last-published-commit.json (on main) records the last breseq commit that was successfully published, so re-running the workflow with no new upstream commits is a cheap no-op.

Triggering a build

Runs automatically once a day. To trigger manually: from the GitHub UI, Actions → "Build and publish breseq-prerelease" → Run workflow. Or via the CLI:

gh workflow run build-and-publish.yml
gh run watch

Previously published package versions are never deleted — each run adds new package files alongside existing ones and re-indexes the channel.

Testing an install

test-environment.yml defines a throwaway environment pulling breseq-prerelease from this channel:

conda env create -f test-environment.yml
conda activate breseq-prerelease-test
breseq --help