``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.

.. code-block:: bash

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

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

Recipe contribution commands
----------------------------

.. _cli-lint:

``lint``
~~~~~~~~

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

.. code-block:: bash

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

See :doc:`linting` for the checks and their remedies.

.. _cli-build:

``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:

.. code-block:: bash

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

The command also owns optional package and container uploads. See
:doc:`building-locally` for local build and isolated-test examples.

.. _cli-dag:

``dag``
~~~~~~~

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

.. code-block:: bash

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

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

.. _cli-dependent:

``dependent``
~~~~~~~~~~~~~

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

.. code-block:: bash

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

.. _cli-clean-cran-skeleton:

``clean-cran-skeleton``
~~~~~~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

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

.. _cli-bioconductor-skeleton:

``bioconductor-skeleton``
~~~~~~~~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

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

See the Bioconductor section of :doc:`guidelines` 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.

.. _cli-autobump:

``autobump``
~~~~~~~~~~~~

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

.. code-block:: bash

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

See :doc:`updating` for filters, hosters, and update behavior.

.. _cli-update-pinning:

``update-pinning``
~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

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

See :ref:`update-pinnings` for the bulk migration workflow.

.. _cli-duplicates:

``duplicates``
~~~~~~~~~~~~~~

Find Bioconda packages that also exist in another configured channel:

.. code-block:: bash

   bioconda-utils duplicates config.yml

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

.. _cli-annotate-build-failures:

``annotate-build-failures``
~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

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

See :ref:`handling-build-failures` for the bulk-run process.

.. _cli-list-build-failures:

``list-build-failures``
~~~~~~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

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

See :ref:`handling-build-failures` for interpreting and resolving the records.

.. _cli-bulk-trigger-ci:

``bulk-trigger-ci``
~~~~~~~~~~~~~~~~~~~

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

.. code-block:: bash

   bioconda-utils bulk-trigger-ci

This command pushes Git history and is only appropriate within
:ref:`bulk-jobs`.

CI artifact and container publication commands
----------------------------------------------

.. _cli-handle-merged-pr:

``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:

.. code-block:: bash

   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 :doc:`build-system` before running
it manually.