{"id":22599597,"url":"https://github.com/singularityhub/shpc-registry","last_synced_at":"2026-01-02T04:00:13.393Z","repository":{"id":50716155,"uuid":"519896622","full_name":"singularityhub/shpc-registry","owner":"singularityhub","description":"A remote registry for Singularity Registry HPC 🖊️","archived":false,"fork":false,"pushed_at":"2025-12-23T04:24:47.000Z","size":4853914,"stargazers_count":15,"open_issues_count":52,"forks_count":21,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-23T16:49:13.274Z","etag":null,"topics":["container-recipes","environment-modules","lmod","shpc","singularity","singularity-hpc"],"latest_commit_sha":null,"homepage":"https://singularityhub.github.io/shpc-registry/","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/singularityhub.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":".github/FUNDING.yml","license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","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},"funding":{"github":"vsoch"}},"created_at":"2022-07-31T22:03:38.000Z","updated_at":"2025-12-22T23:44:42.000Z","dependencies_parsed_at":"2023-12-19T02:26:09.401Z","dependency_job_id":"26be7141-fabe-4abe-9dd5-6594e0c107eb","html_url":"https://github.com/singularityhub/shpc-registry","commit_stats":null,"previous_names":[],"tags_count":42,"template":false,"template_full_name":null,"purl":"pkg:github/singularityhub/shpc-registry","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/singularityhub%2Fshpc-registry","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/singularityhub%2Fshpc-registry/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/singularityhub%2Fshpc-registry/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/singularityhub%2Fshpc-registry/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/singularityhub","download_url":"https://codeload.github.com/singularityhub/shpc-registry/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/singularityhub%2Fshpc-registry/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28168747,"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","status":"online","status_checked_at":"2026-01-02T02:00:06.235Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["container-recipes","environment-modules","lmod","shpc","singularity","singularity-hpc"],"created_at":"2024-12-08T11:10:36.080Z","updated_at":"2026-01-02T04:00:13.299Z","avatar_url":"https://github.com/singularityhub.png","language":"Shell","readme":"# Singularity HPC Registry\n\nThis is the main remote registry for [Singularity HPC](https://github.com/singularityhub/singularity-hpc).\n\n[![DOI](https://zenodo.org/badge/519896622.svg)](https://zenodo.org/badge/latestdoi/519896622)\n\n📖️ Read the [documentation](https://singularity-hpc.readthedocs.io/en/latest/) 📖️\n⭐️ Browse the [container module collection](https://singularityhub.github.io/shpc-registry/) ⭐️\n\n## Contribution\n\nThis registry showcases Singularity HPC (shpc), and provides the default set of containers for its default registry.\nContributions are very much welcome, so please do submit a pull-request if you'd like more software to be added, or open an issue to request a new addition!\n\nThe documentation has an [introduction](https://singularity-hpc.readthedocs.io/en/latest/getting_started/developer-guide.html#writing-registry-entries) about registries, and explains how to organize the required files for a container entry.\n\n### Automated generation\n\nFirst of all, there is an automated way of getting most of the `container.yaml` written via GitHub magic 🎩 automation.\n\n1. [Fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) of this repository.\n2. Go to the Actions tab.\n3. Select \"Generate New Container\" in the left-hand side menu.\n4. Click the \"Run workflow\" dropdown on the right-hand side.\n5. Fill in the name of the container you want to build a `container.yaml` for, as well as a URL and a description (both are mandatory fields). Leave the branch as `main`.\n6. Hit the green \"Run workflow\" button, wait and marvel at the magic :sparkles: happening. The GitHub Action will automatically open a pull request with most of the `container.yaml` filled in for you. You can check the branch out, edit it further – in particular refine the list aliases.\n\n### Updates\n\nNote that all of these scripts registry singularity-hpc (shpc) to be installed:\n\n```bash\n$ pip install singularity-hpc\n```\n\n#### Aliases\n\nIf you find a container missing aliases (or having extras) and you don't want to manually open files,\nwe provide a helper script to do so. After cloning the repository, you could check out a new branch and add an alias \n(note the `--registry` defaults to the present working directory where you are running the script, so this\nshould be run in the root of the cloned repository):\n\n```bash\n$ python .github/scripts/alias.py add quay.io/biocontainers/samtools test /opt/bin/test\n```\n\nIf you ask to add an alias that already exists, this might mean changing the path, and you need to\nuse force:\n\n```bash\n$ python .github/scripts/alias.py add quay.io/biocontainers/samtools test /opt/bin/test --force\n```\n\nAnd then to remove:\n\n```bash\n$ python .github/scripts/alias.py remove quay.io/biocontainers/samtools test\n```\n\nIf an alias doesn't exist, you will get an error on remove.\nAfter these changes you would want to open a pull request to persist your changes to the registry.\n\n#### Features\n\nThe equivalent helper exists for features. As an example, here is how to set a boolean\n(true/false) or value of None):\n\n```bash\n$ python .github/scripts/feature.py add quay.io/biocontainers/samtools home true\n$ python .github/scripts/feature.py add quay.io/biocontainers/samtools home false\n$ python .github/scripts/feature.py add quay.io/biocontainers/samtools home none\n```\n\nAnd how to remove it:\n\n```bash\n$ python .github/scripts/feature.py remove quay.io/biocontainers/samtools home\n```\n\nAnd then to remove:\n\n```bash\n$ python .github/scripts/alias.py remove quay.io/biocontainers/samtools test /opt/bin/test\n```\n\nThe same rule applies for using `--force`.\n\n#### Environment\n\nAnd finally, we have the same for environment. Here are examples:\n\n```bash\n$ python .github/scripts/env.py add quay.io/biocontainers/samtools maintainer vsoch\n$ python .github/scripts/env.py remove quay.io/biocontainers/samtools maintainer\n```\n\n### BioContainers\n\nWe have a [script](.github/scripts/get_biocontainers.py) that will generate (non existing) modules for BioContainers,\nand it is run once a week! It works by way of using an updated cache at [https://github.com/singularityhub/shpc-registry-cache]\ngenerated directly from Biocontainers, which not only captures aliases for a latest tag, but also derives the accumulated\ncounts across all 8K+ containers. With these counts we can generate aliases as follows:\n\n- Start with the loaded global counts, counts.json\n- Subset to those in a container, the alias counts\n- Rank ordering from least to greatest (lower frequency is a more unique commands we are interested in) \n- Including any counts with a frequency \u003c= 10 (this accounts for containers with many unique aliases) `--min-count-inclusion`\n- Above that threshold, including the next N `--additional-count-inclusion` (less unique but possibly important or interesting)\n- Use these to generate a new container.yaml for the file (if it does not exist yet!)\n\nTo run the above, you'll need the cache cloned locally, and singularity-hpc installed\n\n```bash\n$ pip install git+https://github.com/singularityhub/singularity-hpc@main\n$ pip install requests pipelib beautifulsoup4\n$ git clone https://github.com/singularityhub/shpc-registry-cache /tmp/cache\n```\n\nAnd then to run the script (this shows the defaults)\n\n```bash\n$ python .github/scripts/get_biocontainers.py --cache /tmp/cache --registry $(pwd) --min-count-inclusion 10 --additional-count-inclusion 25\n```\n\nfrom the root. Since this added over 8K containers to the registry, we needed a new strategy for running the updater TBA!\n\n\n### Expected content\n\nRefer to the documentation for a list of the [`container.yaml` fields](https://singularity-hpc.readthedocs.io/en/latest/getting_started/developer-guide.html#registry-yaml-fields), especially the _required_ ones.\nA pull-request that doesn't contain the required fields will have changes requested to add them.\n\nThis registry is only for container images freely available. We can't accept `container.yaml` for private or access-restricted containers.\n\nFurthermore, consider the following tips when making the pull-request:\n\n- Ideally, the container tags listed in `container.yaml` should be actual versions, not generic `latest`, `stable`, which tend to be moving targets. Remember that containers and Singularity HPC are there for reproducibility !\n- The convention here is to put containers hosted on the Docker Hub at the top of the repository, e.g. [ruby](https://github.com/singularityhub/shpc-registry/tree/main/ruby), rather than in a `docker.io` sub-directory.\n- By putting your name down as `author`, you accept you may be contacted to review further updates of the `container.yaml`\n\n## 😁️ Contributors 😁️\n\nWe use the [all-contributors](https://github.com/all-contributors/all-contributors)\ntool to generate a contributors graphic below.\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --\u003e\n\u003c!-- prettier-ignore-start --\u003e\n\u003c!-- markdownlint-disable --\u003e\n\u003ctable\u003e\n  \u003ctbody\u003e\n    \u003ctr\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://vsoch.github.io\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/814322?v=4?s=100\" width=\"100px;\" alt=\"Vanessasaurus\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eVanessasaurus\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=vsoch\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/audreystott\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/43943628?v=4?s=100\" width=\"100px;\" alt=\"Audrey Stott\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eAudrey Stott\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=audreystott\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"alecbcs.com\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/19558067?v=4?s=100\" width=\"100px;\" alt=\"Alec Scott\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eAlec Scott\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=alecbcs\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/manbat\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/41646490?v=4?s=100\" width=\"100px;\" alt=\"manbat\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003emanbat\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=manbat\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/marcodelapierre\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/16972180?v=4?s=100\" width=\"100px;\" alt=\"Marco De La Pierre\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eMarco De La Pierre\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=marcodelapierre\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"http://surak.wordpress.com\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/878399?v=4?s=100\" width=\"100px;\" alt=\"Alexandre Strube\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eAlexandre Strube\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=surak\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca 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align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://muffato.github.io\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/623458?v=4?s=100\" width=\"100px;\" alt=\"Matthieu Muffato\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eMatthieu Muffato\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=muffato\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/georgiastuart\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/8276147?v=4?s=100\" width=\"100px;\" alt=\"Georgia Stuart\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eGeorgia Stuart\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=georgiastuart\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      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href=\"https://github.com/singularityhub/shpc-registry/commits?author=AlexisEspinosaGayosso\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n      \u003ctd align=\"center\" valign=\"top\" width=\"14.28%\"\u003e\u003ca href=\"https://github.com/georgiesamaha\"\u003e\u003cimg src=\"https://avatars.githubusercontent.com/u/73086054?v=4?s=100\" width=\"100px;\" alt=\"Georgie Samaha\"/\u003e\u003cbr /\u003e\u003csub\u003e\u003cb\u003eGeorgie Samaha\u003c/b\u003e\u003c/sub\u003e\u003c/a\u003e\u003cbr /\u003e\u003ca href=\"https://github.com/singularityhub/shpc-registry/commits?author=georgiesamaha\" title=\"Code\"\u003e💻\u003c/a\u003e\u003c/td\u003e\n    \u003c/tr\u003e\n  \u003c/tbody\u003e\n\u003c/table\u003e\n\n\u003c!-- markdownlint-restore --\u003e\n\u003c!-- prettier-ignore-end --\u003e\n\n\u003c!-- ALL-CONTRIBUTORS-LIST:END --\u003e\n\n\n## License\n\nThis code is licensed under the MPL 2.0 [LICENSE](LICENSE).\n","funding_links":["https://github.com/sponsors/vsoch"],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsingularityhub%2Fshpc-registry","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsingularityhub%2Fshpc-registry","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsingularityhub%2Fshpc-registry/lists"}