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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
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
Data Storage and Retrieval
- BioServices
ReadDatastores(Dependency mismatch with BioAlignments)