vireosnp.def

BootStrap: docker
From: ubuntu:latest


%post


    apt-get update
    apt-get dist-upgrade -y
    apt-get install -y wget
    apt-get install -y unzip
    apt-get install -y git
    apt-get install -y curl    
    apt-get clean

    ## zlib
    apt-get install -y zlib1g-dev

    ## g++
    apt-get install -y build-essential

    # miniconda
    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
    bash Miniconda3-latest-Linux-x86_64.sh -f -b -p /opt/conda
    . /opt/conda/etc/profile.d/conda.sh
    conda activate base
    conda update --yes --all
    conda create -n app python=3.7
    conda activate app
    conda config --add channels conda-forge
    conda config --add channels bioconda
    conda config --add channels r

    # install vireoSNP

    #conda install matplotlib
#    pip uninstall --yes matplotlib
#    pip install matplotlib==3.0.3 vireoSNP==0.4.2
#    conda install --yes matplotlib=3.0.3 vireoSNP=0.4.2
wget https://github.com/huangyh09/vireo/archive/master.zip
unzip master.zip
cd vireo-master

python setup.py install

    # create bind points for NIH HPC environment
    mkdir /gpfs /spin1 /data /scratch /fdb /lscratch /vf
    for i in $(seq 1 20); do ln -s /gpfs/gsfs$i /gs$i; done

    # clean up
    apt-get clean
    conda clean --yes --all

%environment
    export LC_ALL=C
    export PATH=/opt/conda/envs/app/bin:$PATH