arcsUVA/cellprofiler:3.1.8

$ singularity pull shub://arcsUVA/cellprofiler:3.1.8

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-wxgtk3.0    \
        python-zmq         \
        python-pytest      \
        libcanberra-gtk-module \
        packagekit-gtk3-module
    
    # CellProfiler
    VERSION=3.1.8
    TARBALL=v${VERSION}.tar.gz
    cd /opt
    wget https://github.com/CellProfiler/CellProfiler/archive/${TARBALL}
    tar xzvf ${TARBALL}
    unset JAVA_TOOL_OPTIONS
    cd CellProfiler-${VERSION}

    pip install \
        boto3==1.9.60 \
        centrosome==1.1.6 \
        docutils==0.14 \
        h5py==2.8.0 \
        inflect==2.1.0 \
        javabridge==1.0.18 \
        joblib==0.13.0 \
        mahotas==1.4.5 \
        matplotlib==2.2.3 \
        mysqlclient==1.3.13 \
        numpy==1.15.4 \
        prokaryote==2.4.1 \
        python-bioformats==1.5.2 \
        pyzmq==15.3.0 \
        raven==6.9.0 \
        requests==2.20.1 \
        scikit-image==0.14.0 \
        scikit-learn==0.20.1 \
        scipy==1.1.0 \
        six==1.11.0 \
        pillow==4.3 \
        networkx==2.2 # has to be <2.3 for Python 2.7

    pip install --editable .
    rm /opt/${TARBALL}

    #pip install \
    #    javabridge==1.0.14 \
    #    numpy==1.12

%runscript
    exec cellprofiler

%help
This container provides the following applications:
    * CellProfiler 3.1.8
    * Python 2.7
    * Java JDK 8

%environment
    export PATH=/opt/CellProfiler-3.1.8:$PATH
    export JAVA_TOOL_OPTIONS="-Xss1280k $JAVA_TOOL_OPTIONS"
    export LC_ALL=C

%labels
    AUTHOR khs3z@virginia.edu

Collection


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Metrics

key value
id /containers/arcsUVA-cellprofiler-3.1.8
collection name arcsUVA/cellprofiler
branch master
tag 3.1.8
commit abf5bad48f285ac6fef5eb3b16afd98d88ea52e6
version (container hash) 518d2cef91454e323dd16d24d99ca01d
build date 2020-06-16T23:23:59.119Z
size (MB) 2000
size (bytes) 948002847
SIF Download URL (please use pull with shub://)
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