{"id":41443664,"url":"https://github.com/cellgeni/dockage","last_synced_at":"2026-01-23T14:59:23.306Z","repository":{"id":130192788,"uuid":"164649636","full_name":"cellgeni/dockage","owner":"cellgeni","description":"Cellgeni Docker files","archived":false,"fork":false,"pushed_at":"2025-11-27T21:28:01.000Z","size":28484,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-11-30T12:11:50.906Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"agpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cellgeni.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,"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":"2019-01-08T12:59:25.000Z","updated_at":"2025-11-27T21:28:04.000Z","dependencies_parsed_at":"2025-04-17T17:22:24.073Z","dependency_job_id":"b42bbe48-ad5d-48b7-ab65-5d5bf6273baa","html_url":"https://github.com/cellgeni/dockage","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cellgeni/dockage","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fdockage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fdockage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fdockage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fdockage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cellgeni","download_url":"https://codeload.github.com/cellgeni/dockage/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cellgeni%2Fdockage/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28694459,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-23T14:15:13.573Z","status":"ssl_error","status_checked_at":"2026-01-23T14:09:05.534Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":"2026-01-23T14:59:23.133Z","updated_at":"2026-01-23T14:59:23.292Z","avatar_url":"https://github.com/cellgeni.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Dockage: mooring of Dockerfiles 🐳\nWelcome to Dockage, a collection of Dockerfiles mainly designed for use in bioinformatic workflows.\n\n## Purpose\nThis repository aims to simplify the process tracking all recipes to assemble our docker images.\nOnce built, these containers can be easily converted to Singularity format and deployed on HPC clusters, offering both portability and reproducibility.\n\n\n## Building Docker Images\nEach subdirectory contains a Dockerfile for a specific tool or toolbox/pipeline. To build a Docker image locally:\n\n1. Navigate to the specific tool’s directory (e.g., dockage/toolName/).\n2. Run the following docker build command:\n```bash\ndocker build -t toolName:version -f Dockerfile.version .\n```\nThis will create a Docker image tagged as `toolName:version` that you can use locally or push to a container registry.\n3. To further convert that image to a singularity container we recommend:\n```bash\nsingularity build toolName-version.sif docker-daemon://toolName:version\n```\n\n\n## Repository Structure\n```\ndockage/\n│\n├── tool1/\n│   ├── Dockerfile         # Dockerfile for the latest version or master branch of the tool\n│   ├── Dockerfile.0.1.2   # Dockerfile for version 0.1.2 of tool1\n│   └── additional-files/  # Optional: supplementary scripts or dependencies\n│...\n│...\n├── scripts/               # Useful scripts for automating the build and conversion process\n│   ├── build.sh           # Example build script for Docker images\n│   └── convert.sh         # Example script for converting Docker images to Singularity\n│\n└── README.md              # Documentation and usage instructions\n```\n\n\n# Considerations when creating images\n\n### 🐍 Python-based images\nMake sure you install `jupyterlab` and `papermill`.\n\n### 🐘 R-based images\nMake sure you install `rstudio`.\n\n### Dockerfile in docker image\nCopy the Dockerfile to the container image as the last step. Add this as the last two lines of your Dockerfile:\n```bash\nCOPY Dockerfile /docker/\nRUN chmod -R 755 /docker\n```\n\n### GPU-base image\nFor best compatiblity with current drivers on the HPC we recommend using:\n```dockerfile\nFROM nvidia/cuda:12.1.1-cudnn8-runtime-ubuntu22.04\n```\n\n### ⚠️ Do not use conda when creating containers\n\n\n# Contributing\nWe welcome contributions! If you have improvements to the existing Dockerfiles or want to add support for more bioinformatics tools, please feel free to open a pull request.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Fdockage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcellgeni%2Fdockage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcellgeni%2Fdockage/lists"}