While the Hummingbird team’s intent is to install Python and R application in the global scope (so others may have access to them), it is sometimes not practical or feasible. In those instances, we instead recommend that users install these libraries in their own home folder as a virtual environment. In that case, the use of conda is required (and often easier).

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

module load miniconda3

While conda is most frequently associated with Python, it is also usable for R installations as well, with a large number of R libraries already built and available for use.

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

conda create -n <env-name>

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

conda activate <env-name>

4. Finally, to install the target software for your environment, 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 the dependencies and versions 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.