TomHarrop/assembly-utils:merqury_45fd3cc

$ singularity pull shub://TomHarrop/assembly-utils:merqury_45fd3cc

Singularity Recipe

Bootstrap: docker
From: ubuntu:19.10

%help
    Container for merqury 45fd3cc
    https://github.com/marbl/merqury

%labels
    MAINTAINER "Tom Harrop"
    VERSION "merqury 45fd3cc"

%environment
    export LC_ALL=C
    export PATH="${PATH}:/meryl/Linux-amd64/bin:/IGV_2.8.0:/merqury"
    export MERQURY="/merqury"

%post
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C
    export PATH="${PATH}:/meryl/Linux-amd64/bin:/IGV_2.8.0:/merqury"
    export MERQURY="/merqury"

    # set up apt
    apt-get clean
    rm -r /var/lib/apt/lists/*
    apt-get  update
    apt-get upgrade -y --fix-missing
    (
        . /etc/os-release
        cat << _EOF_ > mirror.txt
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME} main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt ${UBUNTU_CODENAME}-security main restricted universe multiverse

_EOF_
        mv /etc/apt/sources.list /etc/apt/sources.list.bak
        cat mirror.txt /etc/apt/sources.list.bak > /etc/apt/sources.list
    )

    # dependencies
    apt-get update
    apt-get install -y \
        bedtools \
        build-essential \
        default-jre \
        git \
        r-cran-ggplot2 \
        r-cran-scales \
        samtools \
        wget

    # install meryl
    git clone https://github.com/marbl/meryl.git /meryl
    cd /meryl || exit 1
    git checkout -f v1.0
    git submodule update --init --recursive
    cd /meryl/src || exit 1
    make

    # install igvtools
    wget -O /IGV.zip \
        --no-check-certificate \
        https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_2.8.0.zip
    unzip /IGV.zip
    rm /IGV.zip

    # install merqury
    git clone https://github.com/marbl/merqury.git /merqury
    cd /merqury || exit 1
    git checkout -f 45fd3cc
    git submodule update --init --recursive

Collection

• Name: TomHarrop/assembly-utils
• License: None

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