centos_singularity22.def

# Copyright (c) 2015-2016, Gregory M. Kurtzer. All rights reserved.
# 
# "Singularity" Copyright (c) 2016, The Regents of the University of California,
# through Lawrence Berkeley National Laboratory (subject to receipt of any
# required approvals from the U.S. Dept. of Energy).  All rights reserved.


BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum

# If you want the updates (available at the bootstrap date) to be installed
# inside the container during the bootstrap instead of the General Availability
# point release (7.x) then uncomment the following line
#UpdateURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/updates/$basearch/

%setup
   mkdir "$SINGULARITY_ROOTFS/mcr"
   mkdir -p "$SINGULARITY_ROOTFS/chm_singularity_test_data/images"
   mkdir -p "$SINGULARITY_ROOTFS/chm_singularity_test_data/labels"
   cp testdata/images/*.png "$SINGULARITY_ROOTFS/chm_singularity_test_data/images"
   cp testdata/labels/*.png "$SINGULARITY_ROOTFS/chm_singularity_test_data/labels"
   cp testdata/testimage.png "$SINGULARITY_ROOTFS/chm_singularity_test_data"
   
   cp mcr_installopts.txt "$SINGULARITY_ROOTFS/mcr"
   cp runscript.sh "$SINGULARITY_ROOTFS/singularity"
   chmod a+rx "$SINGULARITY_ROOTFS/singularity"
   VERSION=`cat VERSION | sed "s/\n//g"`
   sed -i "s/@@VERSION@@/$VERSION/g" "$SINGULARITY_ROOTFS/singularity"
   if [ -e MCR_R2013a_glnxa64_installer.zip ] ; then
     echo "Matlab compiled runtime found in current directory. Copying to image"
     cp MCR_R2013a_glnxa64_installer.zip "$SINGULARITY_ROOTFS"
   fi

%post
    echo "Hello from inside the container"
    yum -y install vim-minimal make python python-devel git wget tar cmake epel-release tcsh unzip java-1.8.0-openjdk libXt libXt-devel java-1.8.0-openjdk-devel java-1.8.0-openjdk-headless libXmu libXmu-devel ImageMagick
    mkdir -p /oasis /projects /data /state/partition1 /scratch /scratch1 /scratch2 /ccdbprod
    cd /
    wget https://www.sci.utah.edu/releases/chm_v2.1.367/chm-compiled-r2013a-2.1.367.tar.gz
    tar -zxf chm-compiled-r2013a-2.1.367.tar.gz
    rm /chm-compiled-r2013a-2.1.367.tar.gz
    if [ ! -e /MCR_R2013a_glnxa64_installer.zip ] ; then
      echo "Downloading Matlab Compiled Runtime"
      wget https://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip
    fi
    unzip -d mcr MCR_R2013a_glnxa64_installer.zip
    cd /mcr
    ./install -inputFile mcr_installopts.txt
    rm /MCR_R2013a_glnxa64_installer.zip
%test
    /singularity verify /tmp