{"id":38544863,"url":"https://github.com/fertiglab/jhpce_scripts_for_cogaps","last_synced_at":"2026-01-17T07:17:29.284Z","repository":{"id":146065850,"uuid":"164156338","full_name":"FertigLab/JHPCE_SCRIPTS_FOR_COGAPS","owner":"FertigLab","description":"Template scripts for running CoGAPS on JHPCE","archived":false,"fork":false,"pushed_at":"2019-01-07T21:07:09.000Z","size":8,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-10-25T15:11:33.902Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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/FertigLab.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2019-01-04T21:26:13.000Z","updated_at":"2019-01-07T21:07:10.000Z","dependencies_parsed_at":"2023-04-23T06:47:19.874Z","dependency_job_id":null,"html_url":"https://github.com/FertigLab/JHPCE_SCRIPTS_FOR_COGAPS","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/FertigLab/JHPCE_SCRIPTS_FOR_COGAPS","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FJHPCE_SCRIPTS_FOR_COGAPS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FJHPCE_SCRIPTS_FOR_COGAPS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FJHPCE_SCRIPTS_FOR_COGAPS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FJHPCE_SCRIPTS_FOR_COGAPS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FertigLab","download_url":"https://codeload.github.com/FertigLab/JHPCE_SCRIPTS_FOR_COGAPS/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FertigLab%2FJHPCE_SCRIPTS_FOR_COGAPS/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28503399,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T06:57:29.758Z","status":"ssl_error","status_checked_at":"2026-01-17T06:56:03.931Z","response_time":85,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2026-01-17T07:17:29.197Z","updated_at":"2026-01-17T07:17:29.267Z","avatar_url":"https://github.com/FertigLab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# JHPCE project manager for submitting CoGAPS runs\n\nThis repository contains a template for running multiple CoGAPS jobs on JHPCE.\n\n## Setup\n\n1) clone repository (change `project_name` to your project name)\n\n```\ngit clone https://github.com/FertigLab/JHPCE_SCRIPTS_FOR_COGAPS.git\nmv JHPCE_SCRIPTS_FOR_COGAPS project_name\ncd project_name\nchmod +x run\n```\n\n2) delete `.git` - you no longer need access to this repository\n\n`rm -rf .git`\n\n3) (optional) Create a new git repository to push your result to\n\n```\ngit init\ngit add -A\ngit commit -m \"first commit message\"\ngit remote add origin https://github.com/username/new_repo\ngit push origin master\n```\n\nYour directory structure should now look like this (if you have `tree` installed you can see this with `tree ..`)\n\n```\n..\n└── project_name\n    ├── README.md\n    ├── run\n    └── scripts\n        ├── job_script.sh\n        └── R_script.R\n```\n\n## Usage\n\nNow that you have the directory structure set up, you can use the run script to submit jobs as follows:\n\n1) modify the parameter values `R_script.R` for your specific case\n2) modify the job parameters in `job_script.sh`\n3) execute `./run run_name run_id`\n\nThis will copy over the scripts and run everything in a new directory called `run_name/run_id`. With these scripts you can quickly fire off multiple runs and all information (including log files) will be stored in a separate, well-structured directory.\n\nInside `R_script.R` and `job_script.sh` you can find instructions on how to modify those files.\n\nFor more information use `./run --help`\n\n## Example\n\nAfter modifying `R_script.R` and `job_script.sh` you might set off a few runs like this:\n\n`./run MySingleCellAnalysis 1`\n\nmodify parameters again\n\n`./run MySingleCellAnalysis 2`\n\nand the result will be a directory like this:\n\n```\n├── MySingleCellAnalysis\n│   ├── run_1\n│   │   ├── logs\n│   │   │   ├── slurm-31515407_1.out\n│   │   │   ├── slurm-31515407_2.out\n│   │   │   └── slurm-31515407_3.out\n│   │   ├── result_1\n│   │   │   └── sc_analysis_result_1.RData\n│   │   ├── result_2\n│   │   │   └── sc_analysis_result_2.RData\n│   │   ├── result_3\n│   │   │   └── sc_analysis_result_3.RData\n│   │   └── scripts\n│   │       ├── job_script.sh\n│   │       └── R_script.R\n│   └── run_2\n│       ├── logs\n│       │   ├── slurm-31558492_1.out\n│       │   ├── slurm-31558492_2.out\n│       ├── result_1\n│       │   └── sc_analysis_result_1.RData\n│       ├── result_2\n│       │   └── sc_analysis_result_2.RData\n│       └── scripts\n│           ├── job_script.sh\n│           └── R_script.R\n```\n\nThe log files are sent to `run_id/logs` and the scripts used to set off the run are sent to `run_id/scripts`. All results are sent to `run_id/result_id` where the\n`CogapsResult` object is saved to an `RData` file. The number of results is determined by how many parameters are being looped over in `R_script.R`.\n\n# Bugs/Suggestions\n\nPlease let me know on Slack or at tomsherman159@gmail.com if there are any bugs in these scripts or if there any features you'd like to see added\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Fjhpce_scripts_for_cogaps","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffertiglab%2Fjhpce_scripts_for_cogaps","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffertiglab%2Fjhpce_scripts_for_cogaps/lists"}