{"id":22021629,"url":"https://github.com/lieberinstitute/jhpce_module_source","last_synced_at":"2025-07-05T02:04:46.178Z","repository":{"id":113732178,"uuid":"154386500","full_name":"LieberInstitute/jhpce_module_source","owner":"LieberInstitute","description":"JHPCE module source files","archived":false,"fork":false,"pushed_at":"2025-05-29T14:23:08.000Z","size":230,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":13,"default_branch":"SLURM","last_synced_at":"2025-07-05T02:04:42.546Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LieberInstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2018-10-23T19:39:13.000Z","updated_at":"2025-05-29T14:23:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"2a39482a-5b1e-4abb-825a-c89f4369b8e9","html_url":"https://github.com/LieberInstitute/jhpce_module_source","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/LieberInstitute/jhpce_module_source","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fjhpce_module_source","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fjhpce_module_source/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fjhpce_module_source/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fjhpce_module_source/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LieberInstitute","download_url":"https://codeload.github.com/LieberInstitute/jhpce_module_source/tar.gz/refs/heads/SLURM","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2Fjhpce_module_source/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263645558,"owners_count":23494005,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-30T06:13:23.050Z","updated_at":"2025-07-05T02:04:46.151Z","avatar_url":"https://github.com/LieberInstitute.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# JHPCE module source\n\nThis 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).\n\nThe configuration files are hosted in the [jhpce_module_config](https://github.com/LieberInstitute/jhpce_module_config) GitHub repository.\n\n# Questions\n\nIf 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).\n\n# Usage\n\nSee the [jhpce_module_config](https://github.com/LieberInstitute/jhpce_module_config#usage) repository.\n\n# Create a new module\n\n__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).\n\n```bash\nmkdir hisat2\n```\n\n__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`.\n\n```bash\nmkdir hisat2/2.2.1\n```\n\n__Step 3.__ Copy and rename the [template README.md](README_template.md)\n\n```bash\ncp README_template.md hisat2/2.2.1/README.md\n```\n\n__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.\n\n__Step 5.__ Make sure that the permissions are set correctly at the end.\n\n```bash\n## Use 7 for group: so Nick and Leo can edit the files\nchmod 775 -R hisat2/2.2.1/\n```\n\n\n# Contributors\n\n## Current\n\n- [Nick Eagles](https://nick-eagles.github.io/)\n- [Leonardo Collado Torres](http://lcolladotor.github.io)\n- [Geo Pertea](https://github.com/gpertea)\n- [Ryan Miller](https://github.com/RyAMiller)\n\n## Former\n\n- [Emily E Burke](https://github.com/emilyburke)\n- [Andrew E Jaffe](http://aejaffe.com/)\n\n# JHPCE location\n\n`/jhpce/shared/libd/core`\n\nUseful aliases for your `~/.bashrc` file:\n\n```bash\n## Creating modules\n# https://lmod.readthedocs.io/en/latest/050_lua_modulefiles.html\nalias modsrc=\"cd /jhpce/shared/libd/core\"\nalias modlua=\"cd /jhpce/shared/libd/modulefiles\"\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fjhpce_module_source","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Fjhpce_module_source","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fjhpce_module_source/lists"}