TomHarrop/align-utils:ngmlr_8d76779

$ singularity pull shub://TomHarrop/align-utils:ngmlr_8d76779

Singularity Recipe

Bootstrap: docker
From: ubuntu:19.10

%help
    NGMLR 8d76779
    https://github.com/philres/ngmlr

%labels
    MAINTAINER "Tom Harrop"
    VERSION "NGMLR 8d76779"

%post
    # faster apt downloads, will it break?
    export DEBIAN_FRONTEND=noninteractive
    (
        . /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
    )

    # deps
    apt-get update
    apt-get install -y \
        build-essential \
        cmake \
        git \
        wget \
        zlib1g-dev

    # download 
    git clone https://github.com/philres/ngmlr.git
    cd ngmlr || exit 1
    git checkout \
        --recurse-submodules --force \
        8d76779

    # build
    mkdir -p build
    cd build || exit 1
    cmake ..
    make
    make install

    # tidy up
    cd ../../ || exit 1
    rm -fr ngmlr

%runscript
    exec /usr/local/bin/ngmlr "$@"

Collection

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

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