{"id":20286096,"url":"https://github.com/biocontainers/auto-mulled","last_synced_at":"2025-06-12T22:35:26.789Z","repository":{"id":146749184,"uuid":"63011737","full_name":"BioContainers/auto-mulled","owner":"BioContainers","description":"Generating Docker containers from bioconda on the fly with Travis cron-job feature.","archived":false,"fork":false,"pushed_at":"2017-06-23T08:57:08.000Z","size":33,"stargazers_count":4,"open_issues_count":3,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-04T04:11:57.252Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioContainers.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}},"created_at":"2016-07-10T18:00:52.000Z","updated_at":"2023-06-23T08:44:20.000Z","dependencies_parsed_at":null,"dependency_job_id":"bea1af4b-f066-4fbb-976a-f750cd45754c","html_url":"https://github.com/BioContainers/auto-mulled","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BioContainers/auto-mulled","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioContainers%2Fauto-mulled","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioContainers%2Fauto-mulled/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioContainers%2Fauto-mulled/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioContainers%2Fauto-mulled/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioContainers","download_url":"https://codeload.github.com/BioContainers/auto-mulled/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioContainers%2Fauto-mulled/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259542114,"owners_count":22873755,"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":"2024-11-14T14:30:59.215Z","updated_at":"2025-06-12T22:35:26.744Z","avatar_url":"https://github.com/BioContainers.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Automatic build of linux containers\n\nThe aim of this project is to utilize [mulled](https://github.com/mulled/mulled) and with this [involucro](https://github.com/involucro/involucro) in an automatic way. Every new package in\nbioconda is build and packaged into a Linux Container (Docker, rkt) and available from [quay.io](https://quay.io/organization/biocontainers).\n\nWe have developed small utilities around this technology stack which is currently included in [`galaxy-lib`](https://github.com/galaxyproject/galaxy-lib). Here is a short introduction:\n\n## Search for containers\n\n```sh\nmulled-search -s deeptools -o biocontainers\n```\n\n## Build all packages from bioconda from the last 24h\n\n```sh\nmulled-build-channel --channel bioconda --namespace biocontainers \\\n    --involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build\n```\n\n## Test all packages from bioconda from the last 24h\n\n\u003e tests will be extracted from the `recipes-dir` - we need to improve it, if you have time get in touch with me :)\n\n```sh\nmulled-build-channel --channel bioconda --namespace biocontainers \\\n    --involucro-path ./involucro --recipes-dir ./bioconda-recipes --diff-hours 25 build\n```\n\n## Building Docker containers for local Conda packages\n\n\u003e we modified the samtools package to version 3.0 to make clear we are using a local version\n\n1. build your recipe\n\n  ```sh\n  conda build recipes/samtools\n  ```\n\n2. index your local builds\n\n  ```sh\n  conda index /home/bag/miniconda2/conda-bld/linux-64/\n  ```\n\n3. build a container for your local package\n\n  ```sh\n  mulled-build build-and-test 'samtools=3.0--0' \\\n    --extra-channel file://home/bag/miniconda2/conda-bld/ --test 'samtools --help'\n  ```\n  The `--0` indicates the build version of the conda package. It is recommended to specify this number otherwise\n  you will override already exsisting images. For python conda packages this extension might look like this `--py35_1`.\n\n## Build, test and push a conda-forge package to biocontainers\n\n\u003e You need to have write access to the biocontainers repository\n\n```sh\nmulled-build build-and-test 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers\n```\n```sh\nmulled-build push 'pandoc=1.17.2--0' --test 'pandoc --help' -n biocontainers\n```\n\nToDo:\n-----\n\n * all bioconda precompiled conda-packages are mirrored to the Galaxy depot\n * extend this concept for conda-forge\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocontainers%2Fauto-mulled","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocontainers%2Fauto-mulled","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocontainers%2Fauto-mulled/lists"}