The UCSF Computation Biology Core (CBI) Software Repository

Setup

Requirements

This repository requires:

Lmod (>= 8.6)

Comments: We're deploying to two different Rocky 8 systems running Lmod 8.7.32 and Bash 4.4.20.

Configure installation (always)

Make sure to set environment variables MODULE_HOME and SOFTWARE_HOME to point to the folders where environment modules and software tools should be installed. For example, on the Wynton HPC environment, these are:

SOFTWARE_HOME=/wynton/home/cbi/shared/software/CBI
MODULE_HOME=/wynton/home/cbi/shared/modulefiles/CBI

and on the C4 environment, they are:

SOFTWARE_HOME=/software/c4/cbi/software
MODULE_HOME=/software/c4/cbi/modulefiles

These are only need to be set during installation. They are not needed when users use the CBI software stack.

Install the CBI repository module (once)

To build the CBI.lua repository module and install it to ${MODULE_HOME}/repos/CBI.lua, do:

$ make install

Configure MODULEPATH for all users

For users to get access to the CBI software stack, the above CBI.lua must be on the MODULEPATH. This can be by prepending folder ${MODULE_HOME}/repos/ to the MODULEPATH environment variable in a /etc/profile.d/ script, e.g.

$ cat /etc/profile.d/lmod_custom.sh
MODULEPATH="/software/c4/cbi/modulefiles/repos:$MODULEPATH"
export MODULEPATH

To verify that CBI.lua can be found, open a new shell and call:

$ module show CBI

Note that this MODULEPATH allows for sibling software stacks next to the CBI stack, i.e. other groups will be able to share their software tools by adding a ${MODULE_HOME}/repos/{GROUP-NAME}.lua.

Install individual CBI software tools

Note: In order to install individual CBI modules and the corresponding software tools, above module load CBI must work.

Here is an example how to install the latest version of the bat software, so that it's available via module load CBI bat.

$ cd CBI/bat/
$ make all

This will download the software, extract it, and install it to ${SOFTWARE_HOME}/bat-<version>/. The corresponding module file will be installed to ${MODULE_HOME}/bat/<version>.lua. Some software like bat is prebuilt for Linux when downloaded, whereas other software like R will be built from source code.

Comment: All modules have been verified to install on the Wynton HPC and the C4 environments. These are both running Rocky 8 and are configured similarly. Some of the software has also been verified to install on Ubuntu 22.04.