centos.def

RELEASE=7
VERSION=$1
echo ""
echo "Setting RELEASE=$RELEASE"
echo "Version: $VERSION"
echo ""

DistType "redhat"
MirrorURL "http://mirror.centos.org/centos-${RELEASE}/${RELEASE}/os/\$basearch/"

Setup
Bootstrap

InstallPkgs yum vim-minimal make python python-devel git wget tar
InstallPkgs cmake epel-release tcsh unzip java-1.8.0-openjdk libXt libXt-devel
InstallPkgs java-1.8.0-openjdk-devel java-1.8.0-openjdk-headless libXmu
InstallPkgs libXmu-devel ImageMagick

InstallFile runscript.sh /singularity

# Set version in runscript.sh
RunCmd "sed -i \"s/@@VERSION@@/$VERSION/g\" /singularity"

# Make directories used on Gordon, Comet, & Rocce
RunCmd "mkdir /oasis"
RunCmd "mkdir /projects"
RunCmd "mkdir /data"
RunCmd "mkdir -p /state/partition1"
RunCmd "mkdir /scratch"
RunCmd "mkdir /scratch1"
RunCmd "mkdir /scratch2"
RunCmd "mkdir /ccdbprod"
# Create directories for test data
RunCmd "mkdir -p /chm_singularity_test_data/images"
RunCmd "mkdir -p /chm_singularity_test_data/labels"
InstallFile testdata/images/1.png /chm_singularity_test_data/images
InstallFile testdata/images/2.png /chm_singularity_test_data/images
InstallFile testdata/labels/1.png /chm_singularity_test_data/labels
InstallFile testdata/labels/2.png /chm_singularity_test_data/labels
InstallFile testdata/testimage.png /chm_singularity_test_data

# Copy over CHM
RunCmd "cd /;wget https://www.sci.utah.edu/releases/chm_v2.1.367/chm-compiled-r2013a-2.1.367.tar.gz"
RunCmd "cd /;tar -zxf chm-compiled-r2013a-2.1.367.tar.gz"

# Copy over MCR_R2013a_glnxa64_installer.zip
RunCmd "cd /;wget https://www.mathworks.com/supportfiles/MCR_Runtime/R2013a/MCR_R2013a_glnxa64_installer.zip"
RunCmd "cd /;unzip -d mcr MCR_R2013a_glnxa64_installer.zip"
InstallFile mcr_installopts.txt /mcr
RunCmd "cd /mcr;ls;./install -inputFile mcr_installopts.txt"

RunCmd "rm -f /MCR_R2013a_glnxa64_installer.zip"
RunCmd "rm -f /chm-compiled-r2013a-2.1.367.tar.gz"

Cleanup