We recommend installing conda using either Miniconda (minimal; faster) or Anaconda (complete distribution).
Once you have conda installed on your machine, ensure the base installation is up to date. Note that this may require
sudo permissions for a shared installation; for example, this can apply when conda is installed into
conda deactivate conda update --name="base" --channel="defaults" conda conda update --name="base" --channel="defaults" --all
Important: Don’t run
conda update --all on an Anaconda installation. This can lead to an unstable base environment.
conda deactivate conda update --name="base" --channel="defaults" conda conda update --name="base" --channel="defaults" anaconda
As of the conda v4.4 update, the recommended activation configuration has changed. Now a profile script must be sourced in
Previously, up to v4.3, the location of the
bin/ directory should be exported into
This method is no longer recommended. Source the activation script instead.
My koopa bootloader handles conda activation automatically, and is recommended for deployment across virtual machine instances.
Also, if you prefer zsh over bash, note that conda also supports that shell (refer to the documentation for configuration).
Set up channels
Ensure that bioconda channels are added in the following order:
conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge
.condarc file should be created that contains the following:
channels: - conda-forge - bioconda - defaults
Note that the
r channel should not be in your
.condarc file. This is no longer recommended.
A list of installed conda environments can be obtained with:
conda env list
There are two ways to create (and activate) an environment:
conda create --name="default" shellcheck conda activate default
conda create --name="default" conda activate default conda install shellcheck
Typically I prefer using the first method, but either approaches work.
An environment can be deactivated with:
Here’s how to remove an environment:
conda env remove --name="default"