Singularity.minimap2

Bootstrap: docker
From: alpine:3.8

%post
    apk update
    apk upgrade
    apk add git make
    apk add bash gcc bzip2-dev libc-dev ncurses-dev openjdk8-jre-base xz-dev zlib-dev
    
    git clone https://github.com/lh3/minimap2 /tmp/minimap2
    cd /tmp/minimap2
    make
    mv /tmp/minimap2/minimap2 /usr/local/bin/
    rm -rf /tmp/minimap2

    wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2 -O /tmp/samtools.tar.bz2
    cd /tmp
    tar xvjf samtools.tar.bz2
    cd samtools-1.8 && ./configure && make && make install

    wget https://github.com/broadinstitute/picard/releases/download/2.18.14/picard.jar -O /usr/local/bin/picard.jar

    wget https://raw.githubusercontent.com/connor-lab/singularity-recipes/master/scripts/picard -O /usr/local/bin/picard
    chmod 775 /usr/local/bin/picard

%labels
    Maintainer m-bull
    Version minimap2-latest