From 3eff3e4cc736900c66e4552d34b101cb07db17e7 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Thu, 31 Mar 2022 10:04:17 -0500 Subject: [PATCH] Rebrand to BioJulia Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> --- .github/workflows/build.yml | 12 +-- README.md | 177 +++++++++++------------------------- 2 files changed, 60 insertions(+), 129 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 40bc415..1c66726 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -43,9 +43,9 @@ jobs: with: push: true tags: | - millironx/juliapro:latest - millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} - quay.io/millironx/juliapro:latest - quay.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} - ghcr.io/millironx/juliapro:latest - ghcr.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} + millironx/biojulia:latest + millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} + quay.io/millironx/biojulia:latest + quay.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} + ghcr.io/millironx/biojulia:latest + ghcr.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} diff --git a/README.md b/README.md index 5fc43b0..34f922f 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,13 @@ -# JuliaPro Docker Image +# BioJulia Docker Image -[![Build Docker](https://github.com/MillironX/docker-JuliaPro/actions/workflows/build.yml/badge.svg)](https://github.com/MillironX/docker-JuliaPro/actions/workflows/build.yml) -[![Unlicense](https://img.shields.io/github/license/MillironX/docker-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/blob/master/LICENSE) -[![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/MillironX/docker-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/tags) -[![Docker Pulls](https://img.shields.io/docker/pulls/millironx/juliapro)](https://hub.docker.com/r/millironx/juliapro) -[![Docker Repository on Quay](https://quay.io/repository/millironx/juliapro/status "Docker Repository on -Quay")](https://quay.io/repository/millironx/juliapro) +[![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) -Remember that clunky [Atom]-based [Julia] distribution that gave Julia LTS a UI -and debugger similar to [Matlab] and already included all the packages you could -possibly think to use? Remember [JuliaPro]? - -This is JuilaPro in a [Docker] image[^1]. +Most of the [BioJulia] ecosystem made available as a single ready-made [Docker] +image. Built on top of my [JuliaPro image]. ## Usage @@ -20,9 +16,9 @@ Registry], and is compatible with [Docker], [Podman], and [Singularity/Apptainer], and probably others. ```bash -docker pull millironx/juliapro:latest -podman pull quay.io/millironx/juliapro:latest -singularity pull docker://ghcr.io/millironx/juliapro:latest +docker pull millironx/biojulia:latest +podman pull quay.io/millironx/biojulia:latest +singularity pull docker://ghcr.io/millironx/biojulia:latest ``` The packages are installed in a depot in `/usr/local/share/julia`, so keep this @@ -34,131 +30,66 @@ on the rationale for this and examples, see ## Included Packages -The following packages were included in JuliaPro as of April 26, 2020 according -to [the Wayback Machine]. A checkmark indicates the package was included in this -image, clear boxes indicate that it couldn't be included. I've included several -other packages that I consider essential today at the bottom of the list. +Everything from my [JuliaPro image], plus -### General Programming +### Programming Libraries -- [x] [DataStructures](https://github.com/JuliaLang/DataStructures.jl) -- [x] [LightGraphs](https://github.com/JuliaGraphs/LightGraphs.jl) -- [ ] ~~[Atom](https://github.com/JunoLab/Atom.jl)~~ (Interop meaningless in - container) -- [x] [JuliaWebAPI](https://github.com/JuliaWeb/JuliaWebAPI.jl) -- [ ] ~~[IJulia](https://github.com/JuliaLang/IJulia.jl)~~ (Soft dependency on - Python, which isn't included in the container) -- [x] [Nettle](https://github.com/staticfloat/Nettle.jl) -- [x] [DSP](https://github.com/JuliaDSP/DSP.jl) -- [x] [NearestNeighbors](https://github.com/KristofferC/NearestNeighbors.jl) -- [x] [Parameters](https://github.com/mauro3/Parameters.jl) -- [x] [ParserCombinator](https://github.com/andrewcooke/ParserCombinator.jl) -- [x] [Libz](https://github.com/BioJulia/Libz.jl) -- [x] [BenchmarkTools](https://github.com/JuliaCI/BenchmarkTools.jl) -- [x] ~~[Rebugger](https://github.com/timholy/Rebugger.jl)~~ (Errors on - precompilation) -- [x] [Debugger](https://github.com/JuliaDebug/Debugger.jl) +- [ ] [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) -### General Math +### Biological Types -- [x] [Calculus](https://github.com/johnmyleswhite/Calculus.jl) -- [x] [DataFrames](https://github.com/JuliaStats/DataFrames.jl) -- [x] [StatsBase](https://github.com/JuliaStats/StatsBase.jl) -- [x] [Distributions](https://github.com/JuliaStats/Distributions.jl) -- [x] [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl) -- [x] [GLM](https://github.com/JuliaStats/GLM.jl) -- [x] [OnlineStats](https://github.com/joshday/OnlineStats.jl) -- [x] [DifferentialEquations](https://github.com/JuliaDiffEq/DifferentialEquations.jl) -- [ ] ~~[SymPy](https://github.com/JuliaPy/SymPy.jl)~~ (No Python in container) -- [x] [KernelDensity](https://github.com/JuliaStats/KernelDensity.jl) -- [x] [Zygote](https://github.com/FluxML/Zygote.jl) +- [ ] [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) -### Optimization +### File Formats -- [x] [Optim](https://github.com/JuliaOpt/Optim.jl) -- [x] [Roots](https://github.com/JuliaMath/Roots.jl) +- [ ] [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) -### Databases +### Analyses -- [x] [JDBC](https://github.com/JuliaDB/JDBC.jl) +- [ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl) +- [ ] [PopGen](https://github.com/BioJulia/PopGen.jl.git) -### Building UIs and Visualization +### Compression Codecs and File Processing -- [ ] ~~[PyPlot](https://github.com/JuliaPy/PyPlot.jl)~~ (No Python in container) -- [x] [Interact](https://github.com/JuliaGizmos/Interact.jl) -- [x] [LaTeXStrings](https://github.com/stevengj/LaTeXStrings.jl) -- [x] [Formatting](https://github.com/JuliaIO/Formatting.jl) -- [x] [Images](https://github.com/JuliaImages/Images.jl) -- [x] [Plots](https://github.com/JuliaPlots/Plots.jl) -- [x] [GR](https://github.com/jheinen/GR.jl) -- [x] [UnicodePlots](https://github.com/Evizero/UnicodePlots.jl) -- [x] [ImageMagick](https://github.com/JuliaIO/ImageMagick.jl) -- [x] [StatsPlots](https://github.com/JuliaPlots/StatsPlots.jl) -- [x] [PGFPlots](https://github.com/JuliaTeX/PGFPlots.jl) +- [ ] [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) -### Deep Learning and Machine Learning +### Data Storage and Retrieval -- [x] [Knet](https://github.com/denizyuret/Knet.jl) -- [x] [Clustering](https://github.com/JuliaStats/Clustering.jl) -- [x] [DecisionTree](https://github.com/bensadeghi/DecisionTree.jl) -- [x] [MLBase](https://github.com/JuliaStats/MLBase.jl) -- [x] [Flux](https://github.com/FluxML/Flux.jl) -- [ ] ~~[TensorFlow](https://github.com/malmaud/TensorFlow.jl)~~ (Dependency - conflict with Flux: opted for Flux over TensorFlow) -- [x] [Metalhead](https://github.com/FluxML/Metalhead.jl) -- [ ] ~~[ScikitLearn](https://github.com/cstjean/ScikitLearn.jl)~~ (No Python in - container) - -### Interoperability with Other Languages - -All interoperability has been lost due to not including the other languages in -this image. - -- [ ] ~~[RCall (Interoperability with R)](https://github.com/JuliaInterop/RCall.jl)~~ -- [ ] ~~[JavaCall (Java)](https://github.com/JuliaInterop/JavaCall.jl)~~ -- [ ] ~~[PyCall (Python)](https://github.com/JuliaPy/PyCall.jl)~~ -- [ ] ~~[Conda (Python dependencies)](https://github.com/JuliaPy/Conda.jl)~~ -- [ ] ~~[JuliaInXL (Microsoft Excel)](https://github.com/JuliaComputing/JuliaInXL)~~ - -### File and Data Formats - -- [x] [JSON](https://github.com/JuliaIO/JSON.jl) -- [x] [JLD2](https://github.com/JuliaIO/JLD2.jl) -- [x] [CSV](https://github.com/JuliaData/CSV.jl) -- [x] [LightXML](https://github.com/JuliaIO/LightXML.jl) -- [x] [StaticArrays](https://github.com/JuliaArrays/StaticArrays.jl) -- [x] [ProtoBuf](https://github.com/JuliaIO/ProtoBuf.jl) -- [ ] ~~[CuArrays](https://github.com/JuliaGPU/CuArrays.jl)~~ (Package - deprecated and depends on GPU hardware) - -### Economics and Finance - -- [x] [QuantEcon](https://github.com/QuantEcon/QuantEcon.jl) -- [x] [BusinessDays](https://github.com/JuliaFinance/BusinessDays.jl) -- [ ] ~~[Bloomberg](https://github.com/milktrader/Bloomberg.jl)~~ (Empty package - -- maybe proprietary?) -- [ ] ~~[Blpapi (Bloomberg connector)](https://juliacomputing.com/docs/blpapi-manual.pdf)~~ (Package unavailable) -- [ ] ~~[Miletus](https://github.com/JuliaComputing/Miletus.jl)~~ (Package old - enough to require more downgrades than I'm comfortable with) - -### My Own Additions - -- [x] [EzXML](https://github.com/JuliaIO/EzXML.jl) -- [x] [JSON3](https://github.com/quinnj/JSON3.jl) -- [x] [YAML](https://github.com/JuliaData/YAML.jl) -- [x] [NLsolve](https://github.com/JuliaNLSolvers/NLsolve.jl) - -[^1]: This image doesn't include Juno, just the curated packages. +- [ ] [BioServices](https://github.com/BioJulia/BioServices.jl) +- [ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl) [`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH -[atom]: https://atom.io +[biojulia]: https://biojulia.net [docker hub]: https://hub.docker.com [docker]: https://www.docker.com [github container registry]: https://ghcr.io -[julia]: https://julialang.org -[juliapro]: https://web.archive.org/web/2/https://juliacomputing.com/products/juliapro -[matlab]: https://www.mathworks.com/matlab +[juliapro image]: https://github.com/MillironX/docker-JuliaPro [podman]: https://podman.io [quay]: https://quay.io [singularity/apptainer]: https://apptainer.org -[the wayback machine]: https://web.archive.org/web/20200426173353/https://juliacomputing.com/products/juliapro#curated-pkgs