johnnygenomics / bioconda-utils Goto Github PK

Utilities for building and managing bioconda recipes.

Installation:

First, note that bioconda-utils requires both python3 and conda-build pre-installed. This means that you likely need to have installed conda via the miniconda3 bundle.

pip install git+https://github.com/bioconda/bioconda-utils.git

See the help for the bioconda-utils command-line interface for details:

bioconda-utils -h

• recipes can be built in a docker container or by the system conda-build using the same infrastructure
• improved log files for easy grepping (e.g., grep BIOCONDA log)
• given a subdag of recipes to build, if one recipe fails then other recipes that depend on it will be skipped (and noted in the log).
• uses the API from conda 2.0+ and in general works with the latest conda-build versions (instead of maintaining our own branch)
• test suite for the build tools
• documentation
• each built package can now be tested in an isolated busybox container thanks to mulled-build and involucro. This will catch issues where a recipe fails to specify libs (e.g., libgcc) in the run dependencies.
• the mulled-build testing also means we get per-package docker containers for free

New version of conda-build? Update DEFAULT_CONDA_BUILD_VERSION in docker_utils.py which is the version used for docker containers, and the version spec in conda-requirements.txt which is used to set up the system environment and will therefore be used for non-docker builds (primarily OSX but will also be used for Linux if --docker is not provided to bioconda-utils build).

For example see #24.