{"id":27004493,"url":"https://github.com/tacc/rgc","last_synced_at":"2025-04-04T06:17:00.686Z","repository":{"id":55008495,"uuid":"157883994","full_name":"TACC/rgc","owner":"TACC","description":"RollingGantryCrane pulls and converts containers to LMOD modules","archived":false,"fork":false,"pushed_at":"2021-10-25T19:10:04.000Z","size":639,"stargazers_count":12,"open_issues_count":18,"forks_count":3,"subscribers_count":9,"default_branch":"master","last_synced_at":"2024-04-16T02:11:42.840Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://tacc.github.io/rgc/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/TACC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-11-16T15:12:11.000Z","updated_at":"2024-04-03T11:00:23.000Z","dependencies_parsed_at":"2022-08-14T09:00:23.473Z","dependency_job_id":null,"html_url":"https://github.com/TACC/rgc","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TACC%2Frgc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TACC%2Frgc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TACC%2Frgc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TACC%2Frgc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TACC","download_url":"https://codeload.github.com/TACC/rgc/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247128738,"owners_count":20888235,"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":"2025-04-04T06:17:00.004Z","updated_at":"2025-04-04T06:17:00.676Z","avatar_url":"https://github.com/TACC.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg align=\"center\" alt=\"rgc_logo\" width=\"300\" src=\"docs/images/rgc_logo.svg\"\u003e\n\nRolling Gantry Crane\n======================================================\n\nPulls containers from either:\n\n- [docker hub](https://hub.docker.com/)\n- [quay.io](https://quay.io/)\n\nand generates [Lmod](https://github.com/TACC/Lmod) modulefiles for use on HPC systems.\n\nWorkflow\n------------------------------------------------------\n\n- Validates each URL\n\t- Looks for name and tag on specified repsoitory\n\t- Excludes packages that are classified as Libraries on bio.tools\n- Pulls data for each URL\n\t- Container\n\t- Metadata from\n\t\t- bio.tools\n\t\t- launchpad\n- Scans programs on each container's `$PATH`\n- Filters out programs based on the following criteria\n\t- Programs exist in baseline images\n\t\t- ubuntu:xenial\n\t\t- centos:7\n\t\t- ubuntu:bionic\n\t\t- continuumio/miniconda:latest\n\t\t- biocontainers/biocontainers:latest\n\t\t- gzynda/build-essential:bionic\n\t- Programs that exist in `-p` percent of images\n- Generates Lmod files with\n\t- Metadata\n\t- Exposed executables\n\nRequirements\n------------------------------------------------------\n\n- docker or singularity\n- python 2 or 3\n\t- tqdm\n\nPlatorms\n------------------------------------------------------\n\n- Linux\n- MacOS\n\nUsage\n------------------------------------------------------\n\n```\nusage: rgc [-h] [-I PATH] [-M PATH] [-C STR] [-P STR] [-r STR]\n           [--modprefix STR] [--cachedir STR] [-L] [-p INT] [-S] [-f] [-d]\n           [-t INT] [--version] [-v]\n           URL [URL ...]\n\nrgc - Pulls containers and generates Lmod modulefiles for use on HPC systems\n\npositional arguments:\n  URL                   Image urls to pull\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -I PATH, --imgdir PATH\n                        Directory used to cache singularity images\n                        [./containers]\n  -M PATH, --moddir PATH\n                        Path to modulefiles [./modulefiles]\n  -C STR, --contact STR\n                        Contact URL(s) in modules separated by \",\"\n                        [https://github.com/TACC/rgc/issues]\n  -P STR, --prefix STR  Prefix string to image directory for when an\n                        environment variable is used - not used by default\n  -r STR, --requires STR\n                        Module prerequisites separated by \",\" []\n  --modprefix STR       Prefix for all module names bwa/1.12 -\u003e\n                        bwa/[prefix]-1.12\n  --cachedir STR        Directory to cache metadata in [~/rgc_cache]\n  -L, --include-libs    Include containers of libraries\n  -p INT, --percentile INT\n                        Exclude programs in \u003e= p% of images [25]\n  -S, --singularity     Images are cached as singularity containers - even\n                        when docker is present\n  -f, --force           Force overwrite the cache\n  -d, --delete-old      Delete unused containers and module files\n  -t INT, --threads INT\n                        Number of concurrent threads to use for pulling [8]\n  --version             show program's version number and exit\n  -v, --verbose         Enable verbose logging\n```\n\nExamples\n------------------------------------------------------\n\nPulling and generating modules for bwa, samtools, and bowtie\n\n```\nrgc biocontainers/bwa:0.7.15 biocontainers/samtools:v1.7.0_cv3 biocontainers/bowtie:v1.1.2_cv3\n```\n\nand if you don't have a system running Lmod, feel free to test in docker\n\n```\n$ docker run --privileged --rm -it gzynda/rgc:latest bash\n\n$ rgc biocontainers/bwa:0.7.15 biocontainers/samtools:v1.7.0_cv3 biocontainers/bowtie:v1.1.2_cv3\n$ module use ${PWD}/modulefiles\n$ module avail\n$ module load bwa\n$ bwa\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftacc%2Frgc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftacc%2Frgc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftacc%2Frgc/lists"}