bioconda-utils command reference

This page is an index of the public bioconda-utils commands. It explains what each command owns and links to the corresponding workflow documentation. The installed command’s --help output is authoritative for all available options in that version.

bioconda-utils --help
bioconda-utils <command> --help

For installation, common arguments, and credentials, start with bioconda-utils.

Recipe contribution commands

lint

Check recipes against Bioconda policy and consistency rules. Select recipes by package name or Git range:

bioconda-utils lint --git-range master...HEAD
bioconda-utils lint recipes/ config.yml --packages samtools

See Linting for the checks and their remedies.

build

Build and test selected recipes. --docker runs conda-build in Bioconda’s build container, while --mulled-build-and-test installs the resulting package in a minimal container and repeats the recipe tests:

bioconda-utils build --docker --mulled-build-and-test \
  --packages samtools --force

The command also owns optional package and container uploads. See Testing Recipes Locally for local build and isolated-test examples.

dag

Export the recipe dependency graph as GML, Graphviz dot, or text. The text format groups recipes by build order:

bioconda-utils dag recipes/ config.yml --packages samtools --format txt

Use --hide-singletons to omit packages without graph relationships.

dependent

List recipes that depend on a package, or dependencies of the selected package:

bioconda-utils dependent recipes/ config.yml \
  --reverse-dependencies samtools

clean-cran-skeleton

Normalize a recipe generated by conda skeleton cran for Bioconda, including removal of Windows-only entries and generated comments:

bioconda-utils clean-cran-skeleton recipes/r-example --no-windows

bioconductor-skeleton

Generate a Bioconductor recipe. --recursive also generates missing R dependencies:

bioconda-utils bioconductor-skeleton limma recipes/ config.yml --recursive

See the Bioconductor section of Guidelines for bioconda recipes for policy and maintenance details.

Repository maintenance commands

These commands are primarily intended for Bioconda maintainers and automation. Review their help and the linked workflow before using options that upload, remove, commit, or push data.

autobump

Scan recipes for new upstream releases and optionally create update pull requests:

bioconda-utils autobump recipes/ config.yml --packages samtools --dry-run

See Updating recipes for filters, hosters, and update behavior.

update-pinning

Increase build numbers for recipes affected by changed dependency pinnings and propagate required rebuilds through the recipe graph:

bioconda-utils update-pinning recipes/ config.yml \
  --packages samtools --max-bumps 20

See Updating pinnings for the bulk migration workflow.

duplicates

Find Bioconda packages that also exist in another configured channel:

bioconda-utils duplicates config.yml

--strict-version and --strict-build control matching. --remove is destructive, requires strict build matching, and requires ANACONDA_TOKEN.

annotate-build-failures

Record a build failure reason and optionally add a recipe to the skiplist:

bioconda-utils annotate-build-failures recipes/example \
  --reason "test timeout" --category "test failure" --skiplist

See Handling build failures for the bulk-run process.

list-build-failures

List recorded recipe failures, optionally filtering by Git range or producing Markdown output:

bioconda-utils list-build-failures recipes/ config.yml \
  --output-format markdown

See Handling build failures for interpreting and resolving the records.

bulk-trigger-ci

Create and push the empty commit used to start a build from the protected bulk branch:

bioconda-utils bulk-trigger-ci

This command pushes Git history and is only appropriate within Managing a bulk run.

CI artifact and container publication commands

handle-merged-pr

Fetch and upload artifacts for a merged bioconda-recipes pull request. If the selected CI artifacts are unavailable, it can fall back to building the recipe locally:

bioconda-utils handle-merged-pr recipes/ config.yml \
  --repo bioconda/bioconda-recipes --git-range master...HEAD

This is an automation command with Anaconda, Quay, GitHub, and CI-provider integration. Use its --help output and Build system before running it manually.