TomHarrop/seq-utils:adapterremoval_2.3.1

$ singularity pull shub://TomHarrop/seq-utils:adapterremoval_2.3.1

Singularity Recipe

Bootstrap: docker
From: ubuntu:20.04

%help
    AdapterRemoval
    https://github.com/mikkelschubert/adapterremoval

%environment
    export LC_ALL=C

%post
    # variable
    export LC_ALL=C
    export DEBIAN_FRONTEND=noninteractive

    # 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 \
        build-essential \
        git \
        libbz2-dev \
        wget \
        zlib1g-dev 

    # Download
    git clone \
        https://github.com/MikkelSchubert/adapterremoval.git \
        /adapterremoval
    (
    cd /adapterremoval || exit 1
    git checkout -f v2.3.1
    git submodule update --init --recursive
    make
    make install
    )

    rm -r /adapterremoval

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

Collection

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

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