TomHarrop/variant-utils:stacks_2.3e

$ singularity pull shub://TomHarrop/variant-utils:stacks_2.3e

Singularity Recipe

Bootstrap: docker
From: ubuntu:19.04

%help

    Container for stacks 2.3e
    http://catchenlab.life.illinois.edu/stacks

%labels

    MAINTAINER "Tom Harrop"
    VERSION "stacks 2.3e"

%post
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C

    # 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 update
    apt install -y \
        build-essential \
        python3 \
        samtools \
        wget \
        zlib1g-dev 

    # set up python
    update-alternatives \
        --install /usr/bin/python \
        python \
        /usr/bin/python3 \
        1

    # download stacks
    wget -O "stacks.tar.gz" \
        http://catchenlab.life.illinois.edu/stacks/source/stacks-2.3e.tar.gz
    mkdir /stacks-install
    tar -zxf stacks.tar.gz \
        -C /stacks-install \
        --strip-components 1
    rm stacks.tar.gz

    (
    cd /stacks-install || exit 1
    # fix the tab-matching error in stacks-integrate-alignments
    sed -i \
        's/grep -oE/grep -oP/g' \
        scripts/stacks-integrate-alignments
    # install
    ./configure \
    && make \
    && make install
    )
    rm -rf /stacks-install

%environment
    export LC_ALL=C

%runscript
    exec perl /usr/local/bin/denovo_map.pl "$@"

Collection


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key value
id /containers/TomHarrop-variant-utils-stacks_2.3e
collection name TomHarrop/variant-utils
branch master
tag stacks_2.3e
commit f86d9f8611d4657d553d4b265c18cb33c50c136d
version (container hash) 968b1affdadacdc125901940eca252f683d4cfb1fa5f66859f0e4156c7cb5af4
build date 2020-03-11T23:20:26.878Z
size (MB) 196.140625
size (bytes) 205668352
SIF Download URL (please use pull with shub://)
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