README.md

JHPCE module source

This repository contains the module source files for modules contributed to JHPCE mostly by members of the R/Bioconductor-powered Team Data Science at the Lieber Institute for Brain Development. Though other people from LIBD can contribute to these modules and request to be added to the lieber_modules user group as detailed here.

The configuration files are hosted in the jhpce_module_config GitHub repository.

Questions

If you have any questions, please send an email to the JHPCE bithelp mailing list described at Ways to Seek Help and Support.

Usage

See the jhpce_module_config 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 version 2.2.1.

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.

mkdir hisat2/2.2.1

Step 3. Copy and rename the template README.md

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 file.

Step 5. Make sure that the permissions are set correctly at the end.

## Use 7 for group: so Nick and Leo can edit the files
chmod 775 -R hisat2/2.2.1/

Contributors

Current

• Nick Eagles
• Leonardo Collado Torres
• Geo Pertea
• Ryan Miller

Former

• Emily E Burke
• Andrew E Jaffe

JHPCE location

/jhpce/shared/libd/core

Useful aliases for your ~/.bashrc file:

## 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"