Note: Bioconda supports only 64-bit Linux and Mac OS.
1. Install conda¶
Bioconda requires the conda package manager to be installed. If you
have an Anaconda Python installation, you already have it. Otherwise,
the best way to install it is with the
package. The Python 3 version is recommended.
On MacOS, run:
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh sh Miniconda3-latest-MacOSX-x86_64.sh
On Linux, run:
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh sh Miniconda3-latest-Linux-x86_64.sh
The conda FAQs explain how it’s easy to use with existing Python installations.
2. Set up channels¶
After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, conda-forge is highest priority).
The conda-forge channel contains many general-purpose packages not already
found in the
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
3. Install packages¶
Browse the packages to see what’s available.
Bioconda is now enabled, so any packages on the bioconda channel can be installed into the current conda environment:
conda install bwa
Or a new environment can be created:
conda create -n aligners bwa bowtie hisat star
4. Join the team¶
We invite all parties interested in adding/editing package recipes to join the bioconda team,
so that their pull requests don’t require merging by the core team or other members. To do
so, please fork our recipes have a read
through the Conda documentation.
If you ping
@bioconda/core in a pull request we will review it and then add you to the team, if you desire.