{"id":46932668,"url":"https://github.com/comorment/containers","last_synced_at":"2026-03-11T05:01:45.711Z","repository":{"id":38349793,"uuid":"351193477","full_name":"comorment/containers","owner":"comorment","description":"CoMorMent-Containers","archived":false,"fork":false,"pushed_at":"2026-02-23T13:04:18.000Z","size":26516,"stargazers_count":36,"open_issues_count":41,"forks_count":11,"subscribers_count":6,"default_branch":"main","last_synced_at":"2026-03-05T19:42:21.601Z","etag":null,"topics":["containers","gwas","polygenic-risk-scores","singularity-containers"],"latest_commit_sha":null,"homepage":"https://www.comorment.uio.no","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/comorment.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"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}},"created_at":"2021-03-24T19:04:05.000Z","updated_at":"2026-02-23T12:53:27.000Z","dependencies_parsed_at":"2022-08-25T01:51:37.490Z","dependency_job_id":"cedac40d-b6d3-4f6f-b117-dd9a44140bed","html_url":"https://github.com/comorment/containers","commit_stats":null,"previous_names":[],"tags_count":51,"template":false,"template_full_name":null,"purl":"pkg:github/comorment/containers","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/comorment%2Fcontainers","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/comorment%2Fcontainers/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/comorment%2Fcontainers/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/comorment%2Fcontainers/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/comorment","download_url":"https://codeload.github.com/comorment/containers/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/comorment%2Fcontainers/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30372125,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-10T21:41:54.280Z","status":"online","status_checked_at":"2026-03-11T02:00:07.027Z","response_time":84,"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":["containers","gwas","polygenic-risk-scores","singularity-containers"],"created_at":"2026-03-11T05:01:45.030Z","updated_at":"2026-03-11T05:01:45.699Z","avatar_url":"https://github.com/comorment.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# COSGAP: COntainerized Statistical Genetics Analysis Pipelines\n\n## Documentation\n\nThe main documentation for COSGAP is hosted at [cosgap.rtfd.io](https://cosgap.readthedocs.io)\n\n\u003e [!WARNING] \n\u003e As of Nov 27, 2025 there is known issue with Git LFS quota on this repository. While this is not resolved please use [this Dropbox link](https://www.dropbox.com/scl/fo/13vobohbhq6ol4u070ak3/AEpZZ07R3AjxVr3OfM6wmGI?rlkey=mji06jak3nkm6sk0xc7owzzyq\u0026st=21yzr7tf\u0026dl=0) to download.\n\n## Project status\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7385621.svg)](https://doi.org/10.5281/zenodo.7385621)\n[![Documentation Status](https://readthedocs.org/projects/cosgap/badge/?version=latest)](https://cosgap.readthedocs.io/en/latest/?badge=latest)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Hadolint](https://github.com/comorment/containers/actions/workflows/docker.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/docker.yml)\n[![Flake8](https://github.com/comorment/containers/actions/workflows/python.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/python.yml)\n[![Docker build \"hello\"](https://github.com/comorment/containers/actions/workflows/docker_build_hello.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/docker_build_hello.yml)\n[![Docker build \"python3\"](https://github.com/comorment/containers/actions/workflows/docker_build_python3.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/docker_build_python3.yml)\n[![Docker build \"gwas\"](https://github.com/comorment/containers/actions/workflows/docker_build_gwas.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/docker_build_gwas.yml)\n[![Docker build \"r\"](https://github.com/comorment/containers/actions/workflows/docker_build_r.yml/badge.svg)](https://github.com/comorment/containers/actions/workflows/docker_build_r.yml)\n\n## Information\n\nThe goal of this GitHub repository (\u003chttps://github.com/comorment/containers\u003e) is to distribute software tools for statistical genetics analysis, alongside their respective reference data and scripts (\"analysis pipelines\") to facilitate the application of these tools. The scope of this project is currently limited to genome-wide association studies (GWAS) and post-GWAS statistical-genetics analyses, including polygenic scoring (PGS). This project builds on earlier work by [Tryggve consortium](https://neic.no/tryggve/),\nwith the most recent major development done as part of the CoMorMent EU H2020 project ([comorment.eu](https://comorment.eu)). For more information see our [paper](https://doi.org/10.1093/bioadv/vbae067), [this presentation](https://www.youtube.com/watch?v=msegdR2vJZs) on PGC WWL meeting (Feb 9, 2024), or our online documentation [here](https://cosgap.readthedocs.io/en/latest/).\n\nFor an overview of available software, see [here](docs/README.md).\n\nMost of these tools are packaged into Docker images (\u003chttps://docs.docker.com/get-started/docker-concepts/the-basics/what-is-an-image/\u003e) and Singularity Image Format files (\u003chttps://github.com/apptainer/sif\u003e), compatible with both Singularity (\u003chttps://sylabs.io/singularity/\u003e) and Apptainer (\u003chttps://apptainer.org\u003e) and shared as [packages](https://github.com/orgs/comorment/packages?repo_name=containers) on GitHub.\nYou can download individual container files as described in the [INSTALL](./INSTALL.md) file.\n\nMany of the tools require additional reference data provided in the [reference](https://github.com/comorment/containers/tree/main/reference).\nCertain reference data can not be made publicly available, in which case we provide access instructions in a separate GitHub repository:\n\u003chttps://github.com/comorment/reference\u003e. This repository is private - please approach your contact within the CoMorMent project to enable your access.\n\nDescription of containers and usage instructions are provided in the [docs](https://github.com/comorment/containers/tree/main/docs) folder.\n\nMore extensive use cases of containers, focusing on real data analysis, are provided in the [usecases](https://github.com/comorment/containers/tree/main/usecases) folder.\n\nThe history of changes is available in the [CHANGELOG](./CHANGELOG.md) file.\n\nIf you would like to contribute to developing these containers, please see the [CONTRIBUTING](CONTRIBUTING.md) file.\n\nAdditional tools are available in separate repositories:\n\n* \u003chttps://github.com/comorment/ldsc\u003e - LD score regression\n* \u003chttps://github.com/comorment/mixer\u003e - cross-trait MiXeR analysis\n* \u003chttps://github.com/comorment/popcorn\u003e - cross-ancestry genetic correlations\n* \u003chttps://github.com/comorment/magma\u003e - MAGMA, LAVA, lava-partitioning tools\n* \u003chttps://github.com/comorment/HDL\u003e - High-Definition Likelihood\n* \u003chttps://github.com/comorment/mtag_container\u003e - Multi-Trait Analysis of GWAS using MTAG\n* \u003chttps://github.com/comorment/ldpred2_ref\u003e - reference files for LDpred2. The tool itself is included in ``r.sif`` ([more info](https://github.com/comorment/containers/tree/main/scripts/pgs)).\n\n## Cite\n\nIf you use the software provided here, please cite our [Zenodo.org](https://zenodo.org) code deposit (change version accordingly):\n```\nOleksandr Frei, Andreas Jangmo, Espen Hagen, bayramakdeniz, ttfiliz, Richard Zetterberg, \u0026 John Shorter. (2024). comorment/containers: Comorment-Containers-v1.8.1 (v1.8.1). Zenodo. https://doi.org/10.5281/zenodo.10782180\n```\n\nBibtex format:\n```\n@software{oleksandr_frei_2024_10782180,\n  author       = {Oleksandr Frei and\n                  Andreas Jangmo and\n                  Espen Hagen and\n                  bayramakdeniz and\n                  ttfiliz and\n                  Richard Zetterberg and\n                  John Shorter},\n  title        = {comorment/containers: Comorment-Containers-v1.8.1},\n  month        = mar,\n  year         = 2024,\n  publisher    = {Zenodo},\n  version      = {v1.8.1},\n  doi          = {10.5281/zenodo.10782180},\n  url          = {https://doi.org/10.5281/zenodo.10782180}\n}\n```\n\nPlease also cite our paper:\n\n```\nBayram Cevdet Akdeniz, Oleksandr Frei, Espen Hagen, Tahir Tekin Filiz, Sandeep Karthikeyan, Joëlle Pasman, Andreas Jangmo, Jacob Bergstedt, John R Shorter, Richard Zetterberg, Joeri Meijsen, Ida Elken Sønderby, Alfonso Buil, Martin Tesli, Yi Lu, Patrick Sullivan, Ole A Andreassen, Eivind Hovig, COSGAP: COntainerized Statistical Genetics Analysis Pipelines, Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae067, \u003chttps://doi.org/10.1093/bioadv/vbae067\u003e\n```\n\nBibtex format:\n```\n@article{10.1093/bioadv/vbae067,\n    author = {Akdeniz, Bayram Cevdet and Frei, Oleksandr and Hagen, Espen and Filiz, Tahir Tekin and Karthikeyan, Sandeep and Pasman, Joëlle and Jangmo, Andreas and Bergstedt, Jacob and Shorter, John R and Zetterberg, Richard and Meijsen, Joeri and Sønderby, Ida Elken and Buil, Alfonso and Tesli, Martin and Lu, Yi and Sullivan, Patrick and Andreassen, Ole A and Hovig, Eivind},\n    title = {COSGAP: COntainerized Statistical Genetics Analysis Pipelines},\n    journal = {Bioinformatics Advances},\n    volume = {4},\n    number = {1},\n    pages = {vbae067},\n    year = {2024},\n    month = {05},\n    abstract = {The collection and analysis of sensitive data in large-scale consortia for statistical genetics is hampered by multiple challenges, due to their non-shareable nature. Time-consuming issues in installing software frequently arise due to different operating systems, software dependencies, and limited internet access. For federated analysis across sites, it can be challenging to resolve different problems, including format requirements, data wrangling, setting up analysis on high-performance computing (HPC) facilities, etc. Easier, more standardized, automated protocols and pipelines can be solutions to overcome these issues. We have developed one such solution for statistical genetic data analysis using software container technologies. This solution, named COSGAP: “COntainerized Statistical Genetics Analysis Pipelines,” consists of already established software tools placed into Singularity containers, alongside corresponding code and instructions on how to perform statistical genetic analyses, such as genome-wide association studies, polygenic scoring, LD score regression, Gaussian Mixture Models, and gene-set analysis. Using provided helper scripts written in Python, users can obtain auto-generated scripts to conduct the desired analysis either on HPC facilities or on a personal computer. COSGAP is actively being applied by users from different countries and projects to conduct genetic data analyses without spending much effort on software installation, converting data formats, and other technical requirements.COSGAP is freely available on GitHub (https://github.com/comorment/containers) under the GPLv3 license.},\n    issn = {2635-0041},\n    doi = {10.1093/bioadv/vbae067},\n    url = {https://doi.org/10.1093/bioadv/vbae067},\n    eprint = {https://academic.oup.com/bioinformaticsadvances/article-pdf/4/1/vbae067/57955150/vbae067.pdf},\n}\n```\n\nNote that this project is now renamed \"COSGAP\", and that the citation info has been updated accordingly.\n\n## Installation\n\nPlease confer the [INSTALL.md](./INSTALL.md) file for installation instructions.\n\n## Legacy\n\nEarlier versions (prior to April 2021) of all containers and reference data were distributed via Google Drive. This is no longer the case, the folder on Google Drive is no longer maintained. All containers and reference data are released through this repository.\n\n## Source files\n\nThe source files for configuring and building the container files provided here are found in the [docker](https://github.com/comorment/containers/tree/main/docker) directory.\nSee the corresponding [README](./docker/README.md) file therein for details.\n\n## Documentation build instructions\n\nThe online documentation hosted at [cosgap.rtfd.io](https://cosgap.readthedocs.io) can be built locally using [Sphinx](https://www.sphinx-doc.org/en/master/) in a conda environment as\n\n```\ncd sphinx-docs/source  # documentation source/config directory\nconda env create -f environment.yml  # creates environment \"sphinx\"\nconda activate sphinx\nmake html  # make html-documentation in $PWD/_build/html/\n```\n\nThe resulting file(s) ``$PWD/_build/html/index.html`` can be viewed in any web browser.\nIn order to make a pdf with the documentation, issue\n\n```\nmake pdflatex\n```\n\nand open ``$PWD/_build/latex/cosgap.pdf`` in a pdf viewer.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomorment%2Fcontainers","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcomorment%2Fcontainers","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcomorment%2Fcontainers/lists"}