Getting Started

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 Miniconda package. The Python 3 version is recommended.

On MacOS, run:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
sh Miniconda3-latest-MacOSX-x86_64.sh

On Linux, run:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Follow the instructions in the installer. If you encounter problems, refer to the Miniconda documentation. You can also join our Gitter channel to ask other users for help.

See also

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 defaults channel.

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.

5. Spread the word

Consider adding a badge to your posters and presentations to promote that a tool can be easily installed from Bioconda.