arcsUVA/cellprofiler:2.2.0

$ singularity pull shub://arcsUVA/cellprofiler:2.2.0

Singularity Recipe

BootStrap: docker
From: ubuntu:xenial
IncludeCmd: yes

%post
    apt-get update
    apt-get -y upgrade
    apt-get -y install     \
        build-essential    \
        cython             \
        git                \
        wget               \
        libmysqlclient-dev \
        libhdf5-dev        \
        libxml2-dev        \
        libxslt1-dev       \
        openjdk-8-jdk      \
        python-dev         \
        python-pip         \
        python-vigra       \
        python-h5py        \
        python-mysqldb     \
        python-scipy       \
        python-wxgtk3.0    \
        python-zmq         \
        python-pytest      \
        libcanberra-gtk-module \
        packagekit-gtk3-module

    # CellProfiler
    VERSION=2.2.0
    TARBALL=${VERSION}.tar.gz
    cd /opt
    wget https://github.com/CellProfiler/CellProfiler/archive/${TARBALL}
    tar xzvf ${TARBALL}
    unset JAVA_TOOL_OPTIONS
    cd CellProfiler-${VERSION}
    # python -m pip install --upgrade pip
    pip install \
        numpy==1.12.0 \
        javabridge==1.0.14 \
        matplotlib==2.2.3 \
        Pillow==4.3
    pip install --editable .
    rm /opt/${TARBALL}

%runscript
    exec cellprofiler

%help
This container provides the following applications:
    * CellProfiler 2.2.0
    * Python 2.7
    * Java JDK 8

%environment
    export PATH=/opt/CellProfiler-2.2.0:$PATH
    export JAVA_TOOL_OPTIONS="-Xss1280k $JAVA_TOOL_OPTIONS"

%labels
    AUTHOR khs3z@virginia.edu

Collection

• Name: arcsUVA/cellprofiler
• License: None

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