TomHarrop/singularity-containers:purge_haplotigs_20181203

$ singularity pull shub://TomHarrop/singularity-containers:purge_haplotigs_20181203

Singularity Recipe

Bootstrap: docker
From: rocker/verse:3.5.1 

%help

    Container for purge_haplotigs
    https://bitbucket.org/mroachawri/purge_haplotigs

%labels

    VERSION "purge_haplotigs 20181203"

%post

    # dependencies
    apt-get update
    apt-get install -y \
        bedtools \
        build-essential \
        fig2dev \
        gnuplot \
        samtools \
        wget \
        zlib1g-dev \
        xfig


    # install minimap2
    wget -O "minimap2.tar.gz" \
        --no-check-certificate \
        https://github.com/lh3/minimap2/archive/v2.11.tar.gz
    mkdir minimap2
    tar -zxf minimap2.tar.gz \
        -C minimap2 \
        --strip-components 1

    cd minimap2 || exit 1
    make
    mv minimap2 /usr/local/bin/

    cd .. || exit 1
    rm -rf minimap2 minimap2.tar.gz

    # install mummer
    wget -O "mummer.tar.gz" \
        --no-check-certificate \
        https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
    mkdir mummer-install
    tar -zxf mummer.tar.gz \
        -C mummer-install \
        --strip-components 1
    cd mummer-install || exit 1
    ./configure && make && make install
    cd .. || exit 1
    rm -rf mummer.tar.gz mummer-install
    ldconfig

    # clone
    git clone https://bitbucket.org/mroachawri/purge_haplotigs.git

%environment

    export PATH="${PATH}:/purge_haplotigs/bin"

%runscript

    exec /purge_haplotigs/bin/purge_haplotigs "$@"

Collection

• Name: TomHarrop/singularity-containers
• License: None

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