TomHarrop/assemblers:spades_3.14.1

$ singularity pull shub://TomHarrop/assemblers:spades_3.14.1

Singularity Recipe

Bootstrap: docker
From: ubuntu:20.04

%help
    Spades 3.14.1
    http://cab.spbu.ru/software/spades/

%labels
    MAINTAINER "Tom Harrop"
    VERSION "Spades 3.14.1"

%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 \
        cmake \
        libbz2-dev \
        python \
        wget \
        zlib1g-dev
        
    # install Spades
    wget -O "spades.tar.gz" \
        --no-check-certificate \
        http://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1.tar.gz
    mkdir spades
    tar -zxf spades.tar.gz \
        -C spades \
        --strip-components 1
    cd spades || exit 1
    PREFIX=/usr/local ./spades_compile.sh
    cd .. || exit 1
    rm -rf spades spades.tar.gz

%runscript

    exec /usr/local/bin/spades.py "$@"

Collection

• Name: TomHarrop/assemblers
• License: None

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