mirror of
https://github.com/MillironX/docker-BioJulia.git
synced 2024-10-18 10:13:10 +00:00
Rebrand to BioJulia
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
This commit is contained in:
parent
c4ec4db8bb
commit
3eff3e4cc7
GPG key ID:
139C07724802BC5D
2 changed files with 60 additions and 129 deletions
12
.github/workflows/build.yml
vendored
12
.github/workflows/build.yml
vendored
|
|
@ -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 }}
|
||||
|
|
|
|||
177
README.md
177
README.md
|
|
@ -1,17 +1,13 @@
|
|||
# JuliaPro Docker Image
|
||||
# BioJulia Docker Image
|
||||
|
||||
[](https://github.com/MillironX/docker-JuliaPro/actions/workflows/build.yml)
|
||||
[](https://github.com/MillironX/docker-JuliaPro/blob/master/LICENSE)
|
||||
[](https://github.com/MillironX/docker-JuliaPro/tags)
|
||||
[](https://hub.docker.com/r/millironx/juliapro)
|
||||
[](https://quay.io/repository/millironx/juliapro)
|
||||
[](https://github.com/MillironX/docker-BioJulia/actions/workflows/build.yml)
|
||||
[](https://github.com/MillironX/docker-BioJulia/blob/master/LICENSE)
|
||||
[](https://github.com/MillironX/docker-BioJulia/tags)
|
||||
[](https://hub.docker.com/r/millironx/biojulia)
|
||||
[](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
|
||||
|
|
|
|||
Loading…
Reference in a new issue