Singularity file for MentaLiST

Singularity

Bootstrap: docker
from: ubuntu:18.04

%environment
    JULIA_PKGDIR="/opt/.julia"
    export JULIA_PKGDIR

%post
    apt-get update
    apt-get install -y ca-certificates wget hdf5-tools
    update-ca-certificates
    wget https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz
    tar -xzf julia-0.6.4-linux-x86_64.tar.gz --no-same-permissions
    rm julia-0.6.4-linux-x86_64.tar.gz
    mv /julia-9d11f62bcb /opt/julia-0.6.4
    chown -R root:root /opt
    ln -s /opt/julia-0.6.4/bin/julia /usr/local/bin/julia
    export JULIA_PKGDIR=/opt/.julia
    julia -e 'Pkg.init()'
    julia -e 'Pkg.add("Bio")'
    julia -e 'Pkg.add("OpenGene")'
    julia -e 'Pkg.add("Logging")'
    julia -e 'Pkg.add("ArgParse")'
    julia -e 'Pkg.add("Lumberjack")'
    julia -e 'Pkg.add("FastaIO")'
    julia -e 'Pkg.add("JLD")'
    julia -e 'Pkg.add("DataStructures")'
    chown -R root:users /opt/.julia
    wget https://github.com/WGS-TB/MentaLiST/archive/v0.2.4.tar.gz
    tar -xzf v0.2.4.tar.gz
    rm v0.2.4.tar.gz
    mv MentaLiST-0.2.4 /opt/MentaLiST-0.2.4
    /opt/MentaLiST-0.2.4/src/mentalist -h

%runscript
 
    exec /opt/MentaLiST-0.2.4/src/mentalist "$@"