https://github.com/lieberinstitute/jhpce_module_source
JHPCE module source files
https://github.com/lieberinstitute/jhpce_module_source
Last synced: about 1 year ago
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JHPCE module source files
- Host: GitHub
- URL: https://github.com/lieberinstitute/jhpce_module_source
- Owner: LieberInstitute
- Created: 2018-10-23T19:39:13.000Z (almost 8 years ago)
- Default Branch: SLURM
- Last Pushed: 2025-05-29T14:23:08.000Z (about 1 year ago)
- Last Synced: 2025-07-05T02:04:42.546Z (about 1 year ago)
- Language: Shell
- Size: 225 KB
- Stars: 0
- Watchers: 13
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# JHPCE module source
This repository contains the [module](https://lmod.readthedocs.io/) source files for modules contributed to [JHPCE](https://jhpce.jhu.edu/) mostly by members of the [R/Bioconductor-powered Team Data Science](https://lcolladotor.github.io) at the [Lieber Institute for Brain Development](https://www.libd.org/). Though other people from LIBD can contribute to these modules and request to be added to the `lieber_modules` user group as detailed [here](https://github.com/LieberInstitute/jhpce_module_config?tab=readme-ov-file#lieber_modules-membership-rules).
The configuration files are hosted in the [jhpce_module_config](https://github.com/LieberInstitute/jhpce_module_config) GitHub repository.
# Questions
If you have any questions, please send an email to the [JHPCE bithelp](mailto:bithelp@lists.johnshopkins.edu) mailing list described at [_Ways to Seek Help and Support_](https://jhpce.jhu.edu/help/help-basics/#ways-to-seek-help-and-support).
# Usage
See the [jhpce_module_config](https://github.com/LieberInstitute/jhpce_module_config#usage) repository.
# Create a new module
__Step 1.__ Create a directory in lowercase with the name of the source you are installing. In this example, we'll install [`HISAT2`](https://daehwankimlab.github.io/hisat2/) version [2.2.1](https://github.com/DaehwanKimLab/hisat2/archive/refs/tags/v2.2.1.tar.gz).
```bash
mkdir hisat2
```
__Step 2.__ Create a nested directory with the version number of the software you are installing. In this example, that would be `2.2.1`.
```bash
mkdir hisat2/2.2.1
```
__Step 3.__ Copy and rename the [template README.md](README_template.md)
```bash
cp README_template.md hisat2/2.2.1/README.md
```
__Step 4.__ Edit the template README.md in the new directory and install the software. Make sure that any information for reproducing the installation process is documented. As an example, check the [hisat2/2.2.1/README.md](hisat2/2.2.1/README.md) file.
__Step 5.__ Make sure that the permissions are set correctly at the end.
```bash
## Use 7 for group: so Nick and Leo can edit the files
chmod 775 -R hisat2/2.2.1/
```
# Contributors
## Current
- [Nick Eagles](https://nick-eagles.github.io/)
- [Leonardo Collado Torres](http://lcolladotor.github.io)
- [Geo Pertea](https://github.com/gpertea)
- [Ryan Miller](https://github.com/RyAMiller)
## Former
- [Emily E Burke](https://github.com/emilyburke)
- [Andrew E Jaffe](http://aejaffe.com/)
# JHPCE location
`/jhpce/shared/libd/core`
Useful aliases for your `~/.bashrc` file:
```bash
## Creating modules
# https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html
alias modsrc="cd /jhpce/shared/libd/core"
alias modlua="cd /jhpce/shared/libd/modulefiles"
```