This Dockerfile is based on Julia 0.6 and installs major packages listed below.
- BioAlignments.jl
- BioSequences.jl
- BioSymbols.jl
- GeneticVariation.jl
- GenomicFeatures.jl
This also installs IJulia.jl and other useful packages for bioinformatics.
To build a new docker image, install Docker and
then run docker build -t biojulia .
.
Once the biojulia image is built, you can run docker run -it --rm biojulia
to
start a Julia session:
$ docker run -it --rm biojulia
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: https://docs.julialang.org
_ _ _| |_ __ _ | Type "?help" for help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.6.0 (2017-06-19 13:05 UTC)
_/ |\__'_|_|_|\__'_| | Official http://julialang.org/ release
|__/ | x86_64-pc-linux-gnu
julia> using BioSequences
julia> seq = dna"ACGTN"
5nt DNA Sequence:
ACGTN
To run your script in the current directory:
$ docker run --rm -v $(pwd):/workdir biojulia myscript.jl
To start Jupyter Notebook:
$ docker run --rm -p 8888:8888 --entrypoint jupyter biojulia notebook --ip=0.0.0.0 --allow-root