Characterisation-Virtual-Laboratory/CharacterisationVL-Software:fiji

$ singularity pull shub://Characterisation-Virtual-Laboratory/CharacterisationVL-Software:fiji

Singularity Recipe

Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
OSVersion:  xenial
Include: apt wget sudo vim build-essential git sudo software-properties-common

%environment
    FIJIPATH=/opt/fiji/Fiji.app
    export PATH=$FIJIPATH:$PATH
 
%post
    echo "*********************************************************"
    echo "Setup and display environment"
    echo "*********************************************************"
    export LC_ALL=en_AU.UTF-8
    export LANGUAGE=en_AU.UTF-8
    export DEBIAN_FRONTEND=noninteractive
    echo $LC_ALL
    echo $LANGUAGE
    echo $DEBIAN_FRONTEND
    echo "*********************************************************"
    echo "Install repositories"
    echo "*********************************************************"
    sed -i 's/main/main restricted universe multiverse/g' /etc/apt/sources.list
    echo "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64 /" > /etc/apt/sources.list.d/cuda.list
    apt-key adv --fetch-keys http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/7fa2af80.pub
    echo "*********************************************************"
    echo "Update repositories and install desktop"
    echo "*********************************************************"
    apt update
    apt upgrade -y
    apt install -y locales
    locale-gen en_AU.UTF-8
    apt install -y wget ubuntu-desktop vim software-properties-common git cmake 
    echo "*********************************************************"
    echo "Installing CUDA"
    echo "*********************************************************"
    apt install -y cuda-9-0
    echo "*********************************************************"
    echo "Installing python dependencies"
    echo "*********************************************************"
    apt install -y python-pip python-pyqt5 pyqt5-dev python-tk
    echo "*********************************************************"
    echo "Installing vglrun and TurboVNC"
    echo "*********************************************************"
    wget https://swift.rc.nectar.org.au:8888/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.1.2_amd64.deb
    dpkg -i turbovnc_2.1.2_amd64.deb
    wget https://swift.rc.nectar.org.au:8888/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.5.2_amd64.deb
    dpkg -i virtualgl_2.5.2_amd64.deb
    apt update
    apt -y upgrade

    echo "================================="
    echo "Downloading Fiji Linux 64bit     "
    echo "================================="
    cd /tmp
    wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip

    echo "================================="
    echo "Extracting Fiji Linux 64 bit "
    echo "================================="    
    unzip -d /opt/fiji/ fiji-linux64.zip


%runscript
    $*

Collection

• Name: Characterisation-Virtual-Laboratory/CharacterisationVL-Software
• License: GNU General Public License v3.0

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