Installing your own software on Uppmax

Uppmax provides many preinstalled tools for use by users. A list can be found at Uppmax Software List, with instructions how to load them.

However, sometimes what you want is not installed, or has conflicts with existing packages. In that case it is best to make an environment (or set of environments) in which to install and run these tools.

Installing tools via Conda

Conda is a package manager that allows installation of many tools, packages, and libraries. In particular, Bioconda provides many popular packages provided by the bioinformatic community (See available packages). The advantage of using this tool is that installation is reduced to a single command, and it takes care of installing dependencies too. Another useful feature is that these tools can be installed into multiple environments, meaning tools that would normally have dependency conflicts can use be installed and used separately by just activating and deactivating their environments.

Conda is available on both Rackham and Bianca.

module load conda/latest
export CONDA_ENVS_PATH=/proj/snic-2019XXX/

Uppmax clusters have a hard limit on inode creation and conda will often be the culprit to why you cannot write to disk anymore if you have space left. Every so often, use:

conda clean -ilpt

Installing tools with Conda

Follow the instructions at Bioconda - Installing packages.

Installation is often as simple as:

conda install bwa

A new environment with multiple tools can be created like so:

conda create -n nextflow-env nf-core nextflow

Once you've made your installation, it's often a good idea to clean up with:

conda clean --all