1. Start by loading the miniconda application from the module system:

module load miniconda3

2. Next, you will need to create a virtual environment to install your packages and libraries into:

conda create -p /hb/groups/<group-folder>/<env-name>

which will create the conda environment in the shared location. We call this WITHOUT a specific Python or R version to create an empty stub directory.

3. In order to interact with the environment, it now needs to be activated via:

conda activate /hb/groups/<group-folder>/<env-name>

4. Finally, to install the target application suite you want to run, you will need to run the command:

conda install [-c <channel-name>] <package-name>

It is important to note that we specifically want to install the target end-point application. This is because conda will automatically solve all the dependencies and version for us. If we try to do this all manually, package-by-package, there is a good chance things will fail to work as desired. To see if the specific package you want to install is available, you can run:

conda search [-c <channel-name>] <package-name>

Note that, in some cases (due to dependency-hell) it will be necessary to load multiple channels (eg conda-forge AND bioconductor, etc.). This can be easily done by just including the additional `-c <channel-name>` in the command. The <channel-name> indicates that there are packages not maintained by the official conda repository, but may be required for proper installation. If you don’t know the <channel-name>, you should refer to the installation instructions of the software package you are installing. The “conda-forge” <channel-name> is most common.

PLEASE send email to hummingbird@ucsc.edu if you encounter any unsolvable problems.