Singularity-BigStitcher

BootStrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/


%runscript
    #!/bin/bash
    /jdk/bin/java -cp /software/bigstitcher.jar net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5
    echo $1
    echo $2

%files
    /groups/scicompsoft/home/preibischs/software/jdk1.8.0_112 jdk

%post
    echo "Hello from inside the container"
    sed -i 's/$/ universe/' /etc/apt/sources.list
    apt-get update
    apt-get -y install git maven
    mkdir /software
    cd /software
    git clone https://github.com/PreibischLab/BigStitcher.git
    cd BigStitcher
    export JAVA_HOME=/jdk/
    mvn -Pfatjar clean package
    bs_version=`cat pom.xml | grep -A 2 "<artifactId>Big" | grep "<version>" | awk -F ">" '{print $2}' | awk -F "<" '{print $1}'`
    cd ..
    cp BigStitcher/target/BigStitcher-$bs_version.jar ./bigstitcher.jar
    rm -rf BigStitcher
    cd ~/
    rm -rf .m2

    apt-get -y remove git maven
    apt autoremove -y
    apt-get clean

%environment
    export PATH=/usr/games:$PATH
    export LC_ALL=C
    export JAVA_HOME=/jdk/