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Dockerfile for BioJulia

docker-biojulia

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