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# BioJulia Docker Image
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[![Build Docker ](https://github.com/MillironX/docker-BioJulia/actions/workflows/build.yml/badge.svg )](https://github.com/MillironX/docker-BioJulia/actions/workflows/build.yml)
[![Unlicense ](https://img.shields.io/github/license/MillironX/docker-BioJulia )](https://github.com/MillironX/docker-BioJulia/blob/master/LICENSE)
[![GitHub tag (latest by date) ](https://img.shields.io/github/v/tag/MillironX/docker-BioJulia )](https://github.com/MillironX/docker-BioJulia/tags)
[![Docker Pulls ](https://img.shields.io/docker/pulls/millironx/biojulia )](https://hub.docker.com/r/millironx/biojulia)
[![Docker Repository on Quay ](https://quay.io/repository/millironx/biojulia/status "Docker Repository on Quay" )](https://quay.io/repository/millironx/biojulia)
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Most of the [BioJulia] ecosystem made available as a single ready-made [Docker]
image. Built on top of my [JuliaPro image].
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## Usage
The image is hosted on [Docker Hub], [Quay], and the [GitHub Container
Registry], and is compatible with [Docker], [Podman], and
[Singularity/Apptainer], and probably others.
```bash
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docker pull millironx/biojulia:latest
podman pull quay.io/millironx/biojulia:latest
singularity pull docker://ghcr.io/millironx/biojulia:latest
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```
The packages are installed in a depot in `/usr/local/share/julia` , so keep this
in mind when overwriting the [`JULIA_DEPOT_PATH`] variable. For more information
on the rationale for this and examples, see
- nf-core tools discussion: < https: // github . com / nf-core / tools / pull / 1317 >
- Alex Peltzer's blog: < https: // apeltzer . github . io / post / 03-julia-lang-nextflow >
## Included Packages
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Everything from my [JuliaPro image], plus
### Programming Libraries
- [ ] [Automa ](https://github.com/BioJulia/Automa.jl )
- [ ] [BioGenerics ](https://github.com/BioJulia/BioGenerics.jl )
- [ ] [BioTools ](https://github.com/BioJulia/BioTools.jl )
- [ ] [PopGenCore ](https://github.com/BioJulia/PopGenCore.jl )
### Biological Types
- [ ] [BioAlignments ](https://github.com/MillironX/BioAlignments.jl )
- [ ] [BioSequences ](https://github.com/BioJulia/BioSequences.jl )
- [ ] [BioStructures ](https://github.com/BioJulia/BioStructures.jl )
- [ ] [BioSymbols ](https://github.com/BioJulia/BioSymbols.jl )
- [ ] [GenomeGraphs ](https://github.com/BioJulia/GenomeGraphs.jl )
- [ ] [IntervalTrees ](https://github.com/BioJulia/IntervalTrees.jl )
- [ ] [SubstitutionModels ](https://github.com/BioJulia/SubstitutionModels.jl )
### File Formats
- [ ] [BED ](https://github.com/BioJulia/BED.jl )
- [ ] [BigBed ](https://github.com/BioJulia/BigBed.jl )
- [ ] [BigWig ](https://github.com/BioJulia/BigWig.jl )
- [ ] [FASTX ](https://github.com/BioJulia/FASTX.jl )
- [ ] [GenomicAnnotations ](https://github.com/BioJulia/GenomicAnnotations.jl )
- [ ] [GenomicFeatures ](https://github.com/BioJulia/GenomicFeatures.jl )
- [ ] [MMTF ](https://github.com/BioJulia/MMTF.jl )
- [ ] [TwoBit ](https://github.com/BioJulia/TwoBit.jl )
- [ ] [VariantCallFormat ](https://github.com/rasmushenningsson/VariantCallFormat.jl )
- [ ] [XAM ](https://github.com/MillironX/XAM.jl )
### Analyses
- [ ] [KmerAnalysis ](https://github.com/BioJulia/KmerAnalysis.jl )
- [ ] [PopGen ](https://github.com/BioJulia/PopGen.jl.git )
### Compression Codecs and File Processing
- [ ] [BGZFStreams ](https://github.com/BioJulia/BGZFStreams.jl )
- [ ] [CodecBase ](https://github.com/bicycle1885/CodecBase.jl )
- [ ] [CodecBzip2 ](https://github.com/bicycle1885/CodecBzip2.jl )
- [ ] [CodecLz4 ](https://github.com/invenia/CodecLz4.jl )
- [ ] [CodecXz ](https://github.com/bicycle1885/CodecXz.jl )
- [ ] [CodecZlib ](https://github.com/bicycle1885/CodecZlib.jl )
- [ ] [CodecZstd ](https://github.com/bicycle1885/CodecZstd.jl )
- [ ] [Indexes ](https://github.com/BioJulia/Indexes.jl )
- [ ] [TranscodingStreams ](https://github.com/JuliaIO/TranscodingStreams.jl )
### Data Storage and Retrieval
- [ ] [BioServices ](https://github.com/BioJulia/BioServices.jl )
- [ ] [ReadDatastores ](https://github.com/BioJulia/ReadDatastores.jl )
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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
[docker]: https://www.docker.com
[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
[quay]: https://quay.io
[singularity/apptainer]: https://apptainer.org