Software
There are three sources for finding and installing software on the cluster: conda, apptainer/singularity and environment modules. Installing software in a cluster environment can be challenging when software needs to be compiled. Using Conda and Containers can help avoid this problem by downloading already compiled software. Gathering the dependencies to compile software can also be challenging in a cluster environment. If there isn’t a conda package from a reputable source for some needed software using conda to install compiling dependencies is often a good option.
You cannot use sudo to install software on a cluster. Users do not have permissions to use the sudo command on the cluster. Please create a support ticket if you feel this is necessary for your work.
Conda
The conda package manager provides a way to create software environments from a large list of software packages.
See Conda for more details.
Container - Apptainer/Singularity
Support for containers (including most Docker containers) is provided by a system installed Apptainer (aka Singularity).
See Containers for more details.
Modules
Environment modules provide software that is prepackaged and can be activated. Modules should not be used on the login node.
List available modules
module availActivate the gatk module
module load gatk/4.5.0.0 Use the gatk command…
Deactivate the module
module unload gatk/4.5.0.0See Interactive Job for how to start an interactive job.