{"id":22621090,"url":"https://github.com/millironx/docker-biojulia","last_synced_at":"2026-05-15T18:31:43.088Z","repository":{"id":103064420,"uuid":"476334245","full_name":"MillironX/docker-BioJulia","owner":"MillironX","description":"BioJulia in a Docker image","archived":false,"fork":false,"pushed_at":"2025-10-16T02:22:13.000Z","size":756,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-17T04:55:19.871Z","etag":null,"topics":["biojulia","docker","julia"],"latest_commit_sha":null,"homepage":"","language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"unlicense","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MillironX.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":"2022-03-31T14:09:14.000Z","updated_at":"2025-10-16T02:22:14.000Z","dependencies_parsed_at":"2023-10-02T02:52:49.006Z","dependency_job_id":"a2bece6c-21b2-4ec3-9cca-cede48bb1bb6","html_url":"https://github.com/MillironX/docker-BioJulia","commit_stats":null,"previous_names":[],"tags_count":84,"template":false,"template_full_name":null,"purl":"pkg:github/MillironX/docker-BioJulia","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MillironX%2Fdocker-BioJulia","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MillironX%2Fdocker-BioJulia/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MillironX%2Fdocker-BioJulia/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MillironX%2Fdocker-BioJulia/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MillironX","download_url":"https://codeload.github.com/MillironX/docker-BioJulia/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MillironX%2Fdocker-BioJulia/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281739020,"owners_count":26553092,"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":"2025-10-30T02:00:06.501Z","response_time":61,"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":["biojulia","docker","julia"],"created_at":"2024-12-08T22:17:43.100Z","updated_at":"2025-10-30T03:38:32.399Z","avatar_url":"https://github.com/MillironX.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioJulia Docker Image\n\n[![Build Docker](https://github.com/MillironX/docker-BioJulia/actions/workflows/build_docker.yml/badge.svg)](https://github.com/MillironX/docker-BioJulia/actions/workflows/build_docker.yml)\n[![Unlicense](https://img.shields.io/github/license/MillironX/docker-BioJulia)](https://github.com/MillironX/docker-BioJulia/blob/master/LICENSE)\n[![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/MillironX/docker-BioJulia)](https://github.com/MillironX/docker-BioJulia/tags)\n[![Docker Pulls](https://img.shields.io/docker/pulls/millironx/biojulia)](https://hub.docker.com/r/millironx/biojulia)\n[![Docker Repository on Quay](https://quay.io/repository/millironx/biojulia/status \"Docker Repository on Quay\")](https://quay.io/repository/millironx/biojulia)\n\nMost of the [BioJulia] ecosystem made available as a single ready-made [Docker]\nimage. Built on top of my [JuliaPro image].\n\nNote: the version of the image refers to the latest version of BioSequences that\nwill resolve in the Pkg environment.\n\n## Usage\n\nThe image is hosted on [Docker Hub], [Quay], and the [GitHub Container\nRegistry], and is compatible with [Docker], [Podman], and\n[Singularity/Apptainer], and probably others.\n\n```bash\ndocker pull millironx/biojulia:latest\npodman pull quay.io/millironx/biojulia:latest\nsingularity pull docker://ghcr.io/millironx/biojulia:latest\n```\n\nThe packages are installed in a depot in `/usr/local/share/julia`, so keep this\nin mind when overwriting the [`JULIA_DEPOT_PATH`] variable. For more information\non the rationale for this and examples, see\n\n- nf-core tools discussion: \u003chttps://github.com/nf-core/tools/pull/1317\u003e\n- Alex Peltzer's blog: \u003chttps://apeltzer.github.io/post/03-julia-lang-nextflow\u003e\n\n## Included Packages\n\nEverything from my [JuliaPro image], minus\n\n- [ ] ~~[Flux](https://github.com/FluxML/Flux.jl)~~\n- [ ] ~~[Metalhead](https://github.com/FluxML/Metalhead.jl)~~\n- [ ] ~~[Knet](https://github.com/denizyuret/Knet.jl)~~\n\nplus\n\n### Programming Libraries\n\n- [x] [Automa](https://github.com/BioJulia/Automa.jl)\n- [x] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)\n- [ ] ~~[BioTools](https://github.com/BioJulia/BioTools.jl)~~ (Dependent on\n  BioSequnces v1. Seriously?)\n- [x] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)\n\n### Biological Types\n\n- [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)\n- [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)\n- ~~[ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)~~ (Dependency mismatch with BioAlignments)\n- [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)\n- ~~[ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)~~ (Dependency mismatch with BioAlignments)\n- [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)\n- [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)\n\n### File Formats\n\n- [x] [BED](https://github.com/BioJulia/BED.jl)\n- [ ] ~~[BigBed](https://github.com/BioJulia/BigBed.jl)~~ (Dependency mismatch\n  with PopGen)\n- [x] [BigWig](https://github.com/BioJulia/BigWig.jl)\n- [x] [FASTX](https://github.com/BioJulia/FASTX.jl)\n- [x] [GenomicAnnotations](https://github.com/BioJulia/GenomicAnnotations.jl)\n- [x] [GenomicFeatures](https://github.com/BioJulia/GenomicFeatures.jl)\n- ~~[ ] [GFF3](https://github.com/BioJulia/GFF3.jl)~~ (Dependency mismatch with FASTX)\n- [x] [MMTF](https://github.com/BioJulia/MMTF.jl)\n- [x] [TwoBit](https://github.com/BioJulia/TwoBit.jl)\n- [x] [VariantCallFormat](https://github.com/rasmushenningsson/VariantCallFormat.jl)\n- [x] [XAM](https://github.com/MillironX/XAM.jl)\n\n### Analyses\n\n- ~~[ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)~~ (Dependency mismatch with BioAlignments)\n- [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)\n- [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl)\n\n### Compression Codecs and File Processing\n\n- [x] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)\n- [x] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)\n- [x] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)\n- [x] [CodecLz4](https://github.com/invenia/CodecLz4.jl)\n- [x] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)\n- [x] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)\n- [x] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)\n- [x] [Indexes](https://github.com/BioJulia/Indexes.jl)\n- [x] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)\n\n### Data Storage and Retrieval\n\n- [x] [BioServices](https://github.com/BioJulia/BioServices.jl)\n- ~~[ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)~~ (Dependency mismatch with BioAlignments)\n\n[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH\n[biojulia]: https://biojulia.net\n[docker hub]: https://hub.docker.com\n[docker]: https://www.docker.com\n[github container registry]: https://ghcr.io\n[juliapro image]: https://github.com/MillironX/docker-JuliaPro\n[podman]: https://podman.io\n[quay]: https://quay.io\n[singularity/apptainer]: https://apptainer.org\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmillironx%2Fdocker-biojulia","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmillironx%2Fdocker-biojulia","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmillironx%2Fdocker-biojulia/lists"}