docker-BioJulia/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

• BioAlignments
• BioSequences
• [ ] BioStructures (Dependency mismatch with BioAlignments)
• BioSymbols
• [ ] GenomeGraphs (Dependency mismatch with BioAlignments)
• IntervalTrees
• SubstitutionModels

File Formats

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

Analyses

• [ ] KmerAnalysis (Dependency mismatch with BioAlignments)
• PopGen
• SequenceVariation

Compression Codecs and File Processing

• BGZFStreams
• CodecBase
• CodecBzip2
• CodecLz4
• CodecXz
• CodecZlib
• CodecZstd
• Indexes
• TranscodingStreams

Data Storage and Retrieval

• BioServices
• [ ] ReadDatastores (Dependency mismatch with BioAlignments)