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Rebrand to BioJulia
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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2 changed files with 60 additions and 129 deletions
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.github/workflows/build.yml
vendored
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.github/workflows/build.yml
vendored
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@ -43,9 +43,9 @@ jobs:
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with:
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push: true
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tags: |
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millironx/juliapro:latest
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millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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quay.io/millironx/juliapro:latest
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quay.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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ghcr.io/millironx/juliapro:latest
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ghcr.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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millironx/biojulia:latest
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millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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quay.io/millironx/biojulia:latest
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quay.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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ghcr.io/millironx/biojulia:latest
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ghcr.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
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177
README.md
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README.md
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@ -1,17 +1,13 @@
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# JuliaPro Docker Image
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# BioJulia Docker Image
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[](https://github.com/MillironX/docker-JuliaPro/actions/workflows/build.yml)
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[](https://github.com/MillironX/docker-JuliaPro/blob/master/LICENSE)
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[](https://github.com/MillironX/docker-JuliaPro/tags)
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[](https://hub.docker.com/r/millironx/juliapro)
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[](https://quay.io/repository/millironx/juliapro)
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[](https://github.com/MillironX/docker-BioJulia/actions/workflows/build.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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Remember that clunky [Atom]-based [Julia] distribution that gave Julia LTS a UI
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and debugger similar to [Matlab] and already included all the packages you could
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possibly think to use? Remember [JuliaPro]?
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This is JuilaPro in a [Docker] image[^1].
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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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## Usage
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@ -20,9 +16,9 @@ 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/juliapro:latest
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podman pull quay.io/millironx/juliapro:latest
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singularity pull docker://ghcr.io/millironx/juliapro:latest
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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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@ -34,131 +30,66 @@ on the rationale for this and examples, see
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## Included Packages
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The following packages were included in JuliaPro as of April 26, 2020 according
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to [the Wayback Machine]. A checkmark indicates the package was included in this
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image, clear boxes indicate that it couldn't be included. I've included several
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other packages that I consider essential today at the bottom of the list.
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Everything from my [JuliaPro image], plus
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### General Programming
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### Programming Libraries
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- [x] [DataStructures](https://github.com/JuliaLang/DataStructures.jl)
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- [x] [LightGraphs](https://github.com/JuliaGraphs/LightGraphs.jl)
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- [ ] ~~[Atom](https://github.com/JunoLab/Atom.jl)~~ (Interop meaningless in
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container)
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- [x] [JuliaWebAPI](https://github.com/JuliaWeb/JuliaWebAPI.jl)
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- [ ] ~~[IJulia](https://github.com/JuliaLang/IJulia.jl)~~ (Soft dependency on
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Python, which isn't included in the container)
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- [x] [Nettle](https://github.com/staticfloat/Nettle.jl)
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- [x] [DSP](https://github.com/JuliaDSP/DSP.jl)
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- [x] [NearestNeighbors](https://github.com/KristofferC/NearestNeighbors.jl)
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- [x] [Parameters](https://github.com/mauro3/Parameters.jl)
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- [x] [ParserCombinator](https://github.com/andrewcooke/ParserCombinator.jl)
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- [x] [Libz](https://github.com/BioJulia/Libz.jl)
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- [x] [BenchmarkTools](https://github.com/JuliaCI/BenchmarkTools.jl)
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- [x] ~~[Rebugger](https://github.com/timholy/Rebugger.jl)~~ (Errors on
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precompilation)
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- [x] [Debugger](https://github.com/JuliaDebug/Debugger.jl)
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- [ ] [Automa](https://github.com/BioJulia/Automa.jl)
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- [ ] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)
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- [ ] [BioTools](https://github.com/BioJulia/BioTools.jl)
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- [ ] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)
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### General Math
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### Biological Types
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- [x] [Calculus](https://github.com/johnmyleswhite/Calculus.jl)
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- [x] [DataFrames](https://github.com/JuliaStats/DataFrames.jl)
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- [x] [StatsBase](https://github.com/JuliaStats/StatsBase.jl)
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- [x] [Distributions](https://github.com/JuliaStats/Distributions.jl)
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- [x] [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl)
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- [x] [GLM](https://github.com/JuliaStats/GLM.jl)
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- [x] [OnlineStats](https://github.com/joshday/OnlineStats.jl)
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- [x] [DifferentialEquations](https://github.com/JuliaDiffEq/DifferentialEquations.jl)
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- [ ] ~~[SymPy](https://github.com/JuliaPy/SymPy.jl)~~ (No Python in container)
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- [x] [KernelDensity](https://github.com/JuliaStats/KernelDensity.jl)
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- [x] [Zygote](https://github.com/FluxML/Zygote.jl)
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- [ ] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
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- [ ] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
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- [ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
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- [ ] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
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- [ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
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- [ ] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
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- [ ] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
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### Optimization
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### File Formats
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- [x] [Optim](https://github.com/JuliaOpt/Optim.jl)
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- [x] [Roots](https://github.com/JuliaMath/Roots.jl)
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- [ ] [BED](https://github.com/BioJulia/BED.jl)
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- [ ] [BigBed](https://github.com/BioJulia/BigBed.jl)
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- [ ] [BigWig](https://github.com/BioJulia/BigWig.jl)
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- [ ] [FASTX](https://github.com/BioJulia/FASTX.jl)
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- [ ] [GenomicAnnotations](https://github.com/BioJulia/GenomicAnnotations.jl)
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- [ ] [GenomicFeatures](https://github.com/BioJulia/GenomicFeatures.jl)
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- [ ] [MMTF](https://github.com/BioJulia/MMTF.jl)
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- [ ] [TwoBit](https://github.com/BioJulia/TwoBit.jl)
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- [ ] [VariantCallFormat](https://github.com/rasmushenningsson/VariantCallFormat.jl)
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- [ ] [XAM](https://github.com/MillironX/XAM.jl)
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### Databases
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### Analyses
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- [x] [JDBC](https://github.com/JuliaDB/JDBC.jl)
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- [ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)
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- [ ] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
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### Building UIs and Visualization
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### Compression Codecs and File Processing
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- [ ] ~~[PyPlot](https://github.com/JuliaPy/PyPlot.jl)~~ (No Python in container)
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- [x] [Interact](https://github.com/JuliaGizmos/Interact.jl)
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- [x] [LaTeXStrings](https://github.com/stevengj/LaTeXStrings.jl)
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- [x] [Formatting](https://github.com/JuliaIO/Formatting.jl)
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- [x] [Images](https://github.com/JuliaImages/Images.jl)
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- [x] [Plots](https://github.com/JuliaPlots/Plots.jl)
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- [x] [GR](https://github.com/jheinen/GR.jl)
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- [x] [UnicodePlots](https://github.com/Evizero/UnicodePlots.jl)
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- [x] [ImageMagick](https://github.com/JuliaIO/ImageMagick.jl)
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- [x] [StatsPlots](https://github.com/JuliaPlots/StatsPlots.jl)
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- [x] [PGFPlots](https://github.com/JuliaTeX/PGFPlots.jl)
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- [ ] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)
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- [ ] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)
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- [ ] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)
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- [ ] [CodecLz4](https://github.com/invenia/CodecLz4.jl)
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- [ ] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)
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- [ ] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)
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- [ ] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)
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- [ ] [Indexes](https://github.com/BioJulia/Indexes.jl)
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- [ ] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)
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### Deep Learning and Machine Learning
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### Data Storage and Retrieval
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- [x] [Knet](https://github.com/denizyuret/Knet.jl)
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- [x] [Clustering](https://github.com/JuliaStats/Clustering.jl)
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- [x] [DecisionTree](https://github.com/bensadeghi/DecisionTree.jl)
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- [x] [MLBase](https://github.com/JuliaStats/MLBase.jl)
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- [x] [Flux](https://github.com/FluxML/Flux.jl)
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- [ ] ~~[TensorFlow](https://github.com/malmaud/TensorFlow.jl)~~ (Dependency
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conflict with Flux: opted for Flux over TensorFlow)
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- [x] [Metalhead](https://github.com/FluxML/Metalhead.jl)
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- [ ] ~~[ScikitLearn](https://github.com/cstjean/ScikitLearn.jl)~~ (No Python in
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container)
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### Interoperability with Other Languages
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All interoperability has been lost due to not including the other languages in
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this image.
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- [ ] ~~[RCall (Interoperability with R)](https://github.com/JuliaInterop/RCall.jl)~~
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- [ ] ~~[JavaCall (Java)](https://github.com/JuliaInterop/JavaCall.jl)~~
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- [ ] ~~[PyCall (Python)](https://github.com/JuliaPy/PyCall.jl)~~
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- [ ] ~~[Conda (Python dependencies)](https://github.com/JuliaPy/Conda.jl)~~
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- [ ] ~~[JuliaInXL (Microsoft Excel)](https://github.com/JuliaComputing/JuliaInXL)~~
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### File and Data Formats
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- [x] [JSON](https://github.com/JuliaIO/JSON.jl)
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- [x] [JLD2](https://github.com/JuliaIO/JLD2.jl)
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- [x] [CSV](https://github.com/JuliaData/CSV.jl)
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- [x] [LightXML](https://github.com/JuliaIO/LightXML.jl)
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- [x] [StaticArrays](https://github.com/JuliaArrays/StaticArrays.jl)
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- [x] [ProtoBuf](https://github.com/JuliaIO/ProtoBuf.jl)
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- [ ] ~~[CuArrays](https://github.com/JuliaGPU/CuArrays.jl)~~ (Package
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deprecated and depends on GPU hardware)
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### Economics and Finance
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- [x] [QuantEcon](https://github.com/QuantEcon/QuantEcon.jl)
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- [x] [BusinessDays](https://github.com/JuliaFinance/BusinessDays.jl)
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- [ ] ~~[Bloomberg](https://github.com/milktrader/Bloomberg.jl)~~ (Empty package
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-- maybe proprietary?)
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- [ ] ~~[Blpapi (Bloomberg connector)](https://juliacomputing.com/docs/blpapi-manual.pdf)~~ (Package unavailable)
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- [ ] ~~[Miletus](https://github.com/JuliaComputing/Miletus.jl)~~ (Package old
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enough to require more downgrades than I'm comfortable with)
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### My Own Additions
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- [x] [EzXML](https://github.com/JuliaIO/EzXML.jl)
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- [x] [JSON3](https://github.com/quinnj/JSON3.jl)
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- [x] [YAML](https://github.com/JuliaData/YAML.jl)
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- [x] [NLsolve](https://github.com/JuliaNLSolvers/NLsolve.jl)
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[^1]: This image doesn't include Juno, just the curated packages.
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- [ ] [BioServices](https://github.com/BioJulia/BioServices.jl)
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- [ ] [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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[atom]: https://atom.io
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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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[julia]: https://julialang.org
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[juliapro]: https://web.archive.org/web/2/https://juliacomputing.com/products/juliapro
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[matlab]: https://www.mathworks.com/matlab
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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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[the wayback machine]: https://web.archive.org/web/20200426173353/https://juliacomputing.com/products/juliapro#curated-pkgs
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