Characterisation-Virtual-Laboratory/CharacterisationVL-Software:crisprcas

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

Singularity Recipe

Bootstrap: shub
From:      Characterisation-Virtual-Laboratory/CharacterisationVL-Software:1804

%labels
    MAINTAINER_NAME  Jay van Schyndel
    MAINTAINER_EMAIL jay.vanschyndel@monash.edu

    APPLICATION_NAME ubuntu
    APPLICATION_VERSION 18.04

    HARDWARE CPU

    LAST_UPDATED 26-APR-2019

%environment
    VIEWER_PATH=/opt/CRISPRCasViewer
    FINDER_PATH=/opt/CRISPRCasFinder/bin
    export PATH=$VIEWER_PATH:$FINDER_PATH:$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 "*********************************************************"
    apt-get install -y software-properties-common
    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic main restricted'
    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates main restricted'
    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic universe'
    apt-add-repository -y 'deb http://us.archive.ubuntu.com/ubuntu/ bionic-updates universe'
    echo "*********************************************************"
    echo "Update repositories and install desktop"
    echo "*********************************************************"
    apt update
    apt upgrade -y
    apt install -y locales apt-utils
    locale-gen en_AU.UTF-8

    echo "================================="
    echo " Installing CRISPRCasFinder      "
    echo "================================="
    cd /opt
    wget -O CRISPRCasFinder.zip  https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CRISPRCasFinder.zip
    unzip CRISPRCasFinder.zip

    cd CRISPRCasFinder
    ./installer_UBUNTU.sh

    #Note: Following came from install script. Added to resolve issues with Perl script.
    cp /opt/CRISPRCasFinder/src/vmatch-2.3.0-Linux_x86_64-64bit/vmatch /opt/CRISPRCasFinder/bin/vmatch2
    cp /opt/CRISPRCasFinder/src/vmatch-2.3.0-Linux_x86_64-64bit/mkvtree /opt/CRISPRCasFinder/bin/mkvtree2
    cp /opt/CRISPRCasFinder/src/vmatch-2.3.0-Linux_x86_64-64bit/vsubseqselect /opt/CRISPRCasFinder/bin/vsubseqselect2


    echo "================================="
    echo " Installing CRISPRCasViewer      "
    echo "================================="
    cd /opt
    wget -O CRISPRCasViewer.zip  https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CRISPRCasViewer.zip
    unzip CRISPRCasViewer.zip
    chmod -R g+rx,o+rx CRISPRCasViewer

%runscript
    $*

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key value
id /containers/Characterisation-Virtual-Laboratory-CharacterisationVL-Software-crisprcas
collection name Characterisation-Virtual-Laboratory/CharacterisationVL-Software
branch master
tag crisprcas
commit a4a84554049a0f8f6b26b896c36795895eafa287
version (container hash) 1747ee596ed819d2cc99376911a2c189
build date 2020-09-16T23:54:02.552Z
size (MB) 4692
size (bytes) 1922924575
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