pva_pvac_vt.def

Bootstrap: docker
From: griffithlab/pvactools:4.2.0


%post
    # update and install dependencies
    apt-get update && apt-get install -y python3-pip python3-dev build-essential git wget cmake g++

    # Install vatools
    pip install vatools

    # Install cyvcf2
    pip install cyvcf2

    # Install bgzip
    pip install bgzip

    # Download bam_readcount_helper.py script
    wget https://raw.githubusercontent.com/griffithlab/pmbio.org/master/assets/scripts/bam_readcount_helper.py -O /usr/local/bin/bam_readcount_helper.py
    chmod +x /usr/local/bin/bam_readcount_helper.py

    # Install bam-readcount
    git clone https://github.com/genome/bam-readcount
    cd bam-readcount
    mkdir build
    cd build
    cmake ..
    make
    cp /bam-readcount/build/bin/bam-readcount /usr/local/bin/
    cd /

    # Clean up
    apt-get clean

    # Install vt
    git clone https://github.com/atks/vt.git
    cd vt
    git submodule update --init --recursive
    make
    make test
    cd /

    # Install samtools
    wget https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2
    tar -xvf htslib-1.20.tar.bz2
    cd htslib-1.20    # and similarly for bcftools and htslib
    ./configure --prefix=/usr/local
    make
    make install
    cd / 

%environment
    export PATH=/usr/local/bin:$PATH
    export PATH=/vt:$PATH

%labels
    Author Willem
    Version 1.0