mbhall88/Singularity_recipes:krakenuniq

$ singularity pull shub://mbhall88/Singularity_recipes:krakenuniq

Singularity Recipe

Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/


%post
    apt update
    apt install -y software-properties-common
    apt-add-repository universe
    apt update
    apt install -y git wget build-essential
    export LC_ALL=C.UTF-8
    export LANG=C.UTF-8
    echo 'export LC_ALL=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
    echo 'export LANG=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
    echo "export PATH=/usr/local:/usr/local/bin:$PATH" >> $SINGULARITY_ENVIRONMENT

    # ================================
    # INSTALL blast tools (dustmasker req. for kraken)
    # ================================
    apt install -y libidn11-dev
    VERSION="2.7.1"
    URL=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"$VERSION"/ncbi-blast-"$VERSION"+-x64-linux.tar.gz
    wget -O - "$URL" | tar xzf -
    cp ncbi*/bin/dustmasker /usr/local/bin/
    rm -rf ncbi-blast*
    cd ~

    # ================================
    # INSTALL jellyfish
    # ================================
    VERSION="1.1.11"
    URL=http://www.cbcb.umd.edu/software/jellyfish/jellyfish-"$VERSION".tar.gz
    wget -O - "$URL" | tar xzf -
    cd jellyfish*
    ./configure --prefix=/usr/local/
    make
    make install

    # ================================
    # INSTALL krakenuniq
    # ================================
    VERSION="0.5.7"
    URL=https://github.com/fbreitwieser/krakenuniq/archive/v"$VERSION".tar.gz
    apt install -y zlib1g-dev
    wget -O - "$URL" | tar xzf -
    cd krakenuniq-"$VERSION"
    echo "export PATH=$(pwd):$PATH" >> $SINGULARITY_ENVIRONMENT
    ./install_krakenuniq.sh -j $(pwd)
    cd ~
    perl -MCPAN -e'install "LWP::Simple"'
    ln -s /krakenuniq-"$VERSION"/krakenuniq /krakenuniq-"$VERSION"/krakenuniq-build /krakenuniq-"$VERSION"/krakenuniq-download /krakenuniq-"$VERSION"/krakenuniq-extract-reads /krakenuniq-"$VERSION"/krakenuniq-filter /krakenuniq-"$VERSION"/krakenuniq-mpa-report /krakenuniq-"$VERSION"/krakenuniq-report /krakenuniq-"$VERSION"/krakenuniq-translate /usr/local/bin/

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Metrics

key value
id /containers/mbhall88-Singularity_recipes-krakenuniq
collection name mbhall88/Singularity_recipes
branch master
tag krakenuniq
commit d76b3062b0eb29334c26e9e614e708c6cedf27d7
version (container hash) c9cacb07202e873d68f324837c8baa01
build date 2019-01-09T15:39:53.455Z
size (MB) 760
size (bytes) 260857887
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
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