TomHarrop/align-utils:samtools_3389c09_htslib_42825b7

$ singularity pull shub://TomHarrop/align-utils:samtools_3389c09_htslib_42825b7

Singularity Recipe

Bootstrap: docker
From: ubuntu:19.10

%help

    samtools 3389c09
    bcftools 034b466
    htslib 42825b7
    http://www.htslib.org/

%labels

    VERSION "samtools 1.9"

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

%environment
    export LC_ALL=C

%post
    # faster apt downloads
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C
    (
        . /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
    )

    # apt dependencies
    apt-get update
    apt-get install -y \
        build-essential \
        git \
        libbz2-dev \
        libcurl4-openssl-dev \
        liblzma-dev \
        libncurses-dev \
        wget \
        zlib1g-dev

    # install releases via github
    git clone \
        https://github.com/samtools/htslib.git \
        /htslib
    cd /htslib || exit 1
    # git checkout -f 2e36fa6
    git fetch origin pull/1059/head:informative_vcf_errors
    git checkout -f informative_vcf_errors
    git submodule update --init --recursive
    make
    make install

    git clone \
        https://github.com/samtools/samtools.git \
        /samtools
    cd /samtools || exit 1
    git checkout -f 3389c09
    git submodule update --init --recursive
    make
    make install

    git clone \
        https://github.com/samtools/bcftools.git \
        /bcftools
    cd /bcftools || exit 1
    git checkout -f 034b466
    git submodule update --init --recursive
    make
    make install

    # tidy up
    rm -rf /htslib /samtools /bcftools

Collection

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

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