mirror of
https://github.com/MillironX/docker-BioJulia.git
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108 lines
5 KiB
Markdown
108 lines
5 KiB
Markdown
# BioJulia Docker Image
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[](https://github.com/MillironX/docker-BioJulia/actions/workflows/build_docker.yml)
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[](https://github.com/MillironX/docker-BioJulia/blob/master/LICENSE)
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[](https://github.com/MillironX/docker-BioJulia/tags)
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[](https://hub.docker.com/r/millironx/biojulia)
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[](https://quay.io/repository/millironx/biojulia)
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Most of the [BioJulia] ecosystem made available as a single ready-made [Docker]
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image. Built on top of my [JuliaPro image].
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Note: the version of the image refers to the latest version of BioSequences that
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will resolve in the Pkg environment.
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## Usage
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The image is hosted on [Docker Hub], [Quay], and the [GitHub Container
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Registry], and is compatible with [Docker], [Podman], and
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[Singularity/Apptainer], and probably others.
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```bash
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docker pull millironx/biojulia:latest
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podman pull quay.io/millironx/biojulia:latest
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singularity pull docker://ghcr.io/millironx/biojulia:latest
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```
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The packages are installed in a depot in `/usr/local/share/julia`, so keep this
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in mind when overwriting the [`JULIA_DEPOT_PATH`] variable. For more information
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on the rationale for this and examples, see
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- nf-core tools discussion: <https://github.com/nf-core/tools/pull/1317>
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- Alex Peltzer's blog: <https://apeltzer.github.io/post/03-julia-lang-nextflow>
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## Included Packages
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Everything from my [JuliaPro image], minus
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- [ ] ~~[Flux](https://github.com/FluxML/Flux.jl)~~
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- [ ] ~~[Metalhead](https://github.com/FluxML/Metalhead.jl)~~
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- [ ] ~~[Knet](https://github.com/denizyuret/Knet.jl)~~
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plus
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### Programming Libraries
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- [x] [Automa](https://github.com/BioJulia/Automa.jl)
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- [x] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)
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- [ ] ~~[BioTools](https://github.com/BioJulia/BioTools.jl)~~ (Dependent on
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BioSequnces v1. Seriously?)
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- [x] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)
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### Biological Types
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- [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
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- [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
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- ~~[ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)~~ (Dependency mismatch with BioAlignments)
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- [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
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- ~~[ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)~~ (Dependency mismatch with BioAlignments)
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- [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
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- [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
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### File Formats
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- [x] [BED](https://github.com/BioJulia/BED.jl)
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- [ ] ~~[BigBed](https://github.com/BioJulia/BigBed.jl)~~ (Dependency mismatch
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with PopGen)
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- [x] [BigWig](https://github.com/BioJulia/BigWig.jl)
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- [x] [FASTX](https://github.com/BioJulia/FASTX.jl)
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- [x] [GenomicAnnotations](https://github.com/BioJulia/GenomicAnnotations.jl)
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- [x] [GenomicFeatures](https://github.com/BioJulia/GenomicFeatures.jl)
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- ~~[ ] [GFF3](https://github.com/BioJulia/GFF3.jl)~~ (Dependency mismatch with FASTX)
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- [x] [MMTF](https://github.com/BioJulia/MMTF.jl)
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- [x] [TwoBit](https://github.com/BioJulia/TwoBit.jl)
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- [x] [VariantCallFormat](https://github.com/rasmushenningsson/VariantCallFormat.jl)
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- [x] [XAM](https://github.com/MillironX/XAM.jl)
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### Analyses
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- ~~[ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)~~ (Dependency mismatch with BioAlignments)
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- [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
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- [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl)
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### Compression Codecs and File Processing
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- [x] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)
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- [x] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)
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- [x] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)
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- [x] [CodecLz4](https://github.com/invenia/CodecLz4.jl)
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- [x] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)
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- [x] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)
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- [x] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)
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- [x] [Indexes](https://github.com/BioJulia/Indexes.jl)
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- [x] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)
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### Data Storage and Retrieval
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- [x] [BioServices](https://github.com/BioJulia/BioServices.jl)
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- ~~[ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)~~ (Dependency mismatch with BioAlignments)
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[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
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[biojulia]: https://biojulia.net
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[docker hub]: https://hub.docker.com
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[docker]: https://www.docker.com
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[github container registry]: https://ghcr.io
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[juliapro image]: https://github.com/MillironX/docker-JuliaPro
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[podman]: https://podman.io
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[quay]: https://quay.io
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[singularity/apptainer]: https://apptainer.org
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