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BioJulia in a Docker image

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MillironX 814f583071 [⚡ AUTOMATED]: Pkg upgrade for 2022-08-16 Files changed:\nM Manifest.toml		2022-08-16 02:10:13 +00:00
.github/workflows	Update tag name to reflect BioSequences version number	2022-04-08 20:27:18 -05:00
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README.md	Add SequenceVariation dependency	2022-07-27 13:04:57 -05:00

README.md

BioJulia Docker Image

Most of the BioJulia ecosystem made available as a single ready-made Docker image. Built on top of my JuliaPro image.

Note: the version of the image refers to the latest version of BioSequences that will resolve in the Pkg environment.

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.

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 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

Everything from my JuliaPro image, minus

~~Flux~~
~~Metalhead~~
~~Knet~~

plus

Programming Libraries

Automa
BioGenerics
~~BioTools~~ (Dependent on BioSequnces v1. Seriously?)
PopGenCore

Biological Types

File Formats

BED
~~BigBed~~ (Dependency mismatch with PopGen)
BigWig
FASTX
GenomicAnnotations
GenomicFeatures
GFF3
MMTF
TwoBit
VariantCallFormat
XAM