https://github.com/henrikbengtsson/cbi-software
A Scientific Software Stack for HPC (CentOS oriented)
https://github.com/henrikbengtsson/cbi-software
Last synced: 28 days ago
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A Scientific Software Stack for HPC (CentOS oriented)
- Host: GitHub
- URL: https://github.com/henrikbengtsson/cbi-software
- Owner: HenrikBengtsson
- Created: 2018-01-31T01:49:58.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2025-04-14T06:32:06.000Z (29 days ago)
- Last Synced: 2025-04-15T01:52:44.795Z (28 days ago)
- Language: Makefile
- Homepage: https://wynton.ucsf.edu/hpc/software/software-repositories.html
- Size: 14.7 MB
- Stars: 5
- Watchers: 2
- Forks: 2
- Open Issues: 32
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://github.com/HenrikBengtsson/CBI-software/actions/workflows/shellcheck.yml)
[](https://github.com/HenrikBengtsson/CBI-software/actions/workflows/luacheck.yml)
# 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:
```sh
SOFTWARE_HOME=/wynton/home/cbi/shared/software/CBI
MODULE_HOME=/wynton/home/cbi/shared/modulefiles/CBI
```
and on the C4 environment, they are:
```sh
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:
```sh
$ 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.
```sh
$ 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:
```sh
$ 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`.
```sh
$ cd CBI/bat/
$ make all
```
This will download the software, extract it, and install it to `${SOFTWARE_HOME}/bat-/`. The corresponding module file will be installed to `${MODULE_HOME}/bat/.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._