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Rebrand to BioJulia

Browse source 
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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Thomas A. Christensen II 2022-03-31 10:04:17 -05:00
parent c4ec4db8bb
commit 3eff3e4cc7
Signed by: millironx
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12
.github/workflows/build.yml vendored
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@ -43,9 +43,9 @@ jobs:
with: with:
push: true push: true
tags: | tags: |
millironx/juliapro:latest millironx/biojulia:latest
millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
quay.io/millironx/juliapro:latest quay.io/millironx/biojulia:latest
quay.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} quay.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}
ghcr.io/millironx/juliapro:latest ghcr.io/millironx/biojulia:latest
ghcr.io/millironx/juliapro:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }} ghcr.io/millironx/biojulia:${{ steps.tag-name.outputs.tag }}-${{ steps.hash.outputs.short }}

177
README.md
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@ -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) [![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-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/blob/master/LICENSE) [![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-JuliaPro)](https://github.com/MillironX/docker-JuliaPro/tags) [![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/juliapro)](https://hub.docker.com/r/millironx/juliapro) [![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/juliapro/status "Docker Repository on [![Docker Repository on Quay](https://quay.io/repository/millironx/biojulia/status "Docker Repository on Quay")](https://quay.io/repository/millironx/biojulia)
Quay")](https://quay.io/repository/millironx/juliapro)
Remember that clunky [Atom]-based [Julia] distribution that gave Julia LTS a UI Most of the [BioJulia] ecosystem made available as a single ready-made [Docker]
and debugger similar to [Matlab] and already included all the packages you could image. Built on top of my [JuliaPro image].
possibly think to use? Remember [JuliaPro]?
This is JuilaPro in a [Docker] image[^1].
## Usage ## Usage
@ -20,9 +16,9 @@ Registry], and is compatible with [Docker], [Podman], and
[Singularity/Apptainer], and probably others. [Singularity/Apptainer], and probably others.
```bash ```bash
docker pull millironx/juliapro:latest docker pull millironx/biojulia:latest
podman pull quay.io/millironx/juliapro:latest podman pull quay.io/millironx/biojulia:latest
singularity pull docker://ghcr.io/millironx/juliapro:latest singularity pull docker://ghcr.io/millironx/biojulia:latest
``` ```
The packages are installed in a depot in `/usr/local/share/julia`, so keep this 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 ## Included Packages
The following packages were included in JuliaPro as of April 26, 2020 according Everything from my [JuliaPro image], plus
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.
### General Programming ### Programming Libraries
- [x] [DataStructures](https://github.com/JuliaLang/DataStructures.jl) - [ ] [Automa](https://github.com/BioJulia/Automa.jl)
- [x] [LightGraphs](https://github.com/JuliaGraphs/LightGraphs.jl) - [ ] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)
- [ ] ~~[Atom](https://github.com/JunoLab/Atom.jl)~~ (Interop meaningless in - [ ] [BioTools](https://github.com/BioJulia/BioTools.jl)
container) - [ ] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)
- [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)
### General Math ### Biological Types
- [x] [Calculus](https://github.com/johnmyleswhite/Calculus.jl) - [ ] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
- [x] [DataFrames](https://github.com/JuliaStats/DataFrames.jl) - [ ] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
- [x] [StatsBase](https://github.com/JuliaStats/StatsBase.jl) - [ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
- [x] [Distributions](https://github.com/JuliaStats/Distributions.jl) - [ ] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
- [x] [HypothesisTests](https://github.com/JuliaStats/HypothesisTests.jl) - [ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
- [x] [GLM](https://github.com/JuliaStats/GLM.jl) - [ ] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
- [x] [OnlineStats](https://github.com/joshday/OnlineStats.jl) - [ ] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.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)
### Optimization ### File Formats
- [x] [Optim](https://github.com/JuliaOpt/Optim.jl) - [ ] [BED](https://github.com/BioJulia/BED.jl)
- [x] [Roots](https://github.com/JuliaMath/Roots.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) - [ ] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)
- [x] [Interact](https://github.com/JuliaGizmos/Interact.jl) - [ ] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)
- [x] [LaTeXStrings](https://github.com/stevengj/LaTeXStrings.jl) - [ ] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)
- [x] [Formatting](https://github.com/JuliaIO/Formatting.jl) - [ ] [CodecLz4](https://github.com/invenia/CodecLz4.jl)
- [x] [Images](https://github.com/JuliaImages/Images.jl) - [ ] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)
- [x] [Plots](https://github.com/JuliaPlots/Plots.jl) - [ ] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)
- [x] [GR](https://github.com/jheinen/GR.jl) - [ ] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)
- [x] [UnicodePlots](https://github.com/Evizero/UnicodePlots.jl) - [ ] [Indexes](https://github.com/BioJulia/Indexes.jl)
- [x] [ImageMagick](https://github.com/JuliaIO/ImageMagick.jl) - [ ] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)
- [x] [StatsPlots](https://github.com/JuliaPlots/StatsPlots.jl)
- [x] [PGFPlots](https://github.com/JuliaTeX/PGFPlots.jl)
### Deep Learning and Machine Learning ### Data Storage and Retrieval
- [x] [Knet](https://github.com/denizyuret/Knet.jl) - [ ] [BioServices](https://github.com/BioJulia/BioServices.jl)
- [x] [Clustering](https://github.com/JuliaStats/Clustering.jl) - [ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.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.
[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH [`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 hub]: https://hub.docker.com
[docker]: https://www.docker.com [docker]: https://www.docker.com
[github container registry]: https://ghcr.io [github container registry]: https://ghcr.io
[julia]: https://julialang.org [juliapro image]: https://github.com/MillironX/docker-JuliaPro
[juliapro]: https://web.archive.org/web/2/https://juliacomputing.com/products/juliapro
[matlab]: https://www.mathworks.com/matlab
[podman]: https://podman.io [podman]: https://podman.io
[quay]: https://quay.io [quay]: https://quay.io
[singularity/apptainer]: https://apptainer.org [singularity/apptainer]: https://apptainer.org
[the wayback machine]: https://web.archive.org/web/20200426173353/https://juliacomputing.com/products/juliapro#curated-pkgs