bioconda / bioconda-common

Common definitions for the bioconda build system

Overview

This repository acts as a central "source of truth" which can be used by various components of the Bioconda build system.

Components

common.sh: contains environment variables that control versions.

install-and-set-up-conda.sh:

• downloads and installs conda using the Mambaforge distribution
• installs bioconda-utils dependencies
• installs the version of bioconda-utils specified in common.sh via pip install

configure-conda.sh: ensures channels are configured correctly.

Typical usage

In practice, a typical CI environment will do the following:

1. Download the files, typically via:

   wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh

2. Run install-and-set-up-conda.sh (which sources common.sh).

3. Use the CI platform's mechanism to cache the conda install dir (which is configured in common.sh).

4. After a cache restore, run configure-conda.sh. The reason for this is that the --system arg for conda config is not supported by mamba, and so the channel config ends up in the home directory which is not cached.