|
On O2, we encourage cluster users to install the packages and software they need. One method to install packages and manage environments is to use conda, which is available through the conda2/4.2.13 module. Conda manages dependencies by default when you install packages, which can make it easier to install software. Packages that can be installed with conda include Python modules, libraries, or executable programs. Conda includes its own version of Python (2.7.12), though you can explicitly request to use Python 3 if you would prefer.
Commonly used commands, examples
Command | Meaning |
|---|---|
module spider conda | shows the versions of conda installed on O2 |
module load conda2/version | loads an individual conda module (replace version with an actual version) |
conda info --envs | see available conda environments |
conda create -n test_env | create conda environment named test_env (name the environment whatever you'd like) |
conda create -n aligners_env bwa bowtie star | create conda environment, and install some packages (bwa, bowtie, and star) on the fly |
source activate test_env | "activate" a conda environment named test_env |
source deactivate | exit current conda environment |
conda-env remove -n test_env | delete a conda environment named test_env |
conda search numpy | search for a package (replace numpy with the package of your choice) |
conda install numpy | install a package, and must be within a conda environment or this command will fail. (replace numpy with the package of your choice) |
Setup
To install packages on O2 using conda, you must first create a conda environment. Environments are simply directories in ~/.conda/envs/ that contain packages you installed. You "source" an environment to use those packages, and can "deactivate" to exit the environment. You can have multiple environments, and can switch between them.
...
The centralized conda installation, available through the conda2/4.2.13 module, includes several channels that we support. Channels are repositories where conda looks for packages. This is done with a centralized .condarc file that contains:
conda-forge
defaults
r
bioconda
The order here matters, as conda will pull packages from channels based upon the channel "priority". For example, the channel listed first in .condarc has the highest priority, and the channel listed last has the lowest priority. This means that if the package you want to install is found in multiple channels in your .condarc, conda will default to installing the version found in the highest priority channel. See here in the conda documentation for more information on channel management.
Conda-forge is a repository of recipes, which are used to build conda packages. The defaults channel is necessary for several dependencies, including conda and conda-build. The r channel contains common R packages, some of which are dependencies for bioconda packagesbioconda packages. Bioconda is a channel geared for bioinformatics packages.
...