Singularity bootstrap for CellProfiler 2.2.0 using CentOS 7.3 minimal host to run on RHEL 6.7 nodes of the UConn Storrs HPC cluster

centos7-cellprofiler-2.2.0.def

# -*- mode: rpm-spec -*-

# Singularity bootstrap for CellProfiler
# Host OS used is CentOS Linux release 7.3.1611 (Core)

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

%runscript
        echo "Running cellprofiler with arguments $*"
        exec /usr/bin/cellprofiler "$@"

%post
        echo "Installing OS dependencies for CellProfiler"
        NUMPY_DEPS="lapack-devel gcc-c++"
        SCIPY_DEPS="atlas-devel python-devel"
        MATPLOTLIB_DEPS="libpng-devel freetype-devel"
        JAVABRIDGE_DEPS="java-1.8.0-openjdk-devel"
        CELLPROFILER_DEPS="wget tar python2-pip mysql-devel wxPython-devel"
        yum -y install epel-release # For python2-pip
        yum -y install $NUMPY_DEPS $SCIPY_DEPS $MATPLOTLIB_DEPS $JAVABRIDGE_DEPS $CELLPROFILER_DEPS

        echo "Installing CellProfiler"
        PN=CellProfiler; V=2.2.0; P=$PN-$V; TARBALL=$V.tar.gz # Gentoo's naming convention
        cd /tmp                 # Download directory
        wget -nc https://github.com/$PN/$PN/archive/$V.tar.gz
        cd /opt                 # CellProfiler install prefix
        test -d $P || tar -xvpf /tmp/$TARBALL
        cd $P
        # Cython is required by centrosome, but the dependency is not
        # pulled in.  Seems like a bug with either centrosome or
        # CellProfiler.
        pip install --upgrade pip
        pip install numpy cython
        pip install -vvv --editable .

        echo "HPC cluster specific mount bind points"
        # See http://singularity.lbl.gov/docs-mount
        mkdir -p /work /scratch/scratch{2,3}
        exit 0

%test
        /usr/bin/cellprofiler -h