Characterisation-Virtual-Laboratory/CharacterisationVL-Software:imod_v4_9_9

$ singularity pull shub://Characterisation-Virtual-Laboratory/CharacterisationVL-Software:imod_v4_9_9

Singularity Recipe

# Copyright (c) 2015-2016, Gregory M. Kurtzer. All rights reserved.
# 
# "Singularity" Copyright (c) 2016, The Regents of the University of California,
# through Lawrence Berkeley National Laboratory (subject to receipt of any
# required approvals from the U.S. Dept. of Energy).  All rights reserved.

BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://au.archive.ubuntu.com/ubuntu/


%runscript
    echo "IMOD container built for CVL"
    echo "For new versions please contact help@cvl.org.au"
    $*

%environment
    export IMOD_DIR=/usr/local/IMOD
    export IMOD_QTLIBDIR=/usr/local/IMOD/qtlib
    export PATH=/usr/local/IMOD/bin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
    export IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug
    export IMOD_JAVADIR=/usr/local/java
    export IMOD_CALIB_DIR=/usr/local/ImodCalib

%post
    echo "*********************************************************"
    echo "Setup and display environment"
    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"
    apt update
    apt upgrade -y
    apt install -y locales wget
    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
    locale-gen en_AU.UTF-8
    apt install -y wget ubuntu-desktop vim software-properties-common git cmake default-jre 
    echo "*********************************************************"
    echo "Installing CUDA"
    apt install -y cuda-8-0
    echo "*********************************************************"
    echo "*********************************************************"
    echo "Installing python dependencies"
    apt install -y python-pip python-pyqt5 pyqt5-dev python-tk
    echo "*********************************************************"
    echo "Installing libjpeg dependencies"
    apt install -y libjpeg-turbo8-*
    apt install -y libjpeg-dev
    apt install -y libjpeg8*
    apt install -y libjpeg62*
    echo "*********************************************************"
    echo "Installing software"
    wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_4.9.9_RHEL6-64_CUDA8.0.sh
    chmod +x imod_4.9.9_RHEL6-64_CUDA8.0.sh
    ./imod_4.9.9_RHEL6-64_CUDA8.0.sh -yes

Collection

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

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