mirror of
https://github.com/MillironX/docker-BioJulia.git
synced 2024-12-22 09:28:17 +00:00
Add README
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
This commit is contained in:
parent
f8fb5eb801
commit
b09db0cb57
1 changed files with 163 additions and 0 deletions
163
README.md
Normal file
163
README.md
Normal file
|
@ -0,0 +1,163 @@
|
|||
# JuliaPro Docker Image
|
||||
|
||||
[![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)
|
||||
|
||||
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].
|
||||
|
||||
## 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
|
||||
docker pull millironx/juliapro:latest
|
||||
podman pull quay.io/millironx/juliapro:latest
|
||||
singularity pull docker://ghcr.io/millironx/juliapro:latest
|
||||
```
|
||||
|
||||
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
|
||||
|
||||
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.
|
||||
|
||||
### General Programming
|
||||
|
||||
- [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)
|
||||
|
||||
### General Math
|
||||
|
||||
- [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)
|
||||
|
||||
### Optimization
|
||||
|
||||
- [x] [Optim](https://github.com/JuliaOpt/Optim.jl)
|
||||
- [x] [Roots](https://github.com/JuliaMath/Roots.jl)
|
||||
|
||||
### Databases
|
||||
|
||||
- [x] [JDBC](https://github.com/JuliaDB/JDBC.jl)
|
||||
|
||||
### Building UIs and Visualization
|
||||
|
||||
- [ ] ~~[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)
|
||||
|
||||
### Deep Learning and Machine Learning
|
||||
|
||||
- [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.
|
||||
|
||||
[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
|
||||
[atom]: https://atom.io
|
||||
[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
|
||||
[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