TomHarrop/singularity-containers:samtools_1.9

$ singularity pull shub://TomHarrop/singularity-containers:samtools_1.9

Singularity Recipe

Bootstrap: docker
From: alpine:3.9

%help

    samtools 1.9
    bcflib 1.9
    htslib 1.9
    http://www.htslib.org/

%labels

    VERSION "samtools 1.9"

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

%post

    # install dependencies
    apk add --update \
        bash \
        build-base \
        bzip2-dev \
        gcc \
        git \
        ncurses-dev \
        wget \
        xz-dev \
        zlib-dev

    # download releases
    mkdir htslib
    wget \
        -O "htslib.tar.bz2" \
        --no-check-certificate \
        https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
    tar -jxf htslib.tar.bz2 \
        -C htslib \
        --strip-components 1
    cd htslib || exit 1
    make
    make install
    cd .. || exit 1
    rm -rf htslib.tar.bz2 htslib

    mkdir samtools
    wget \
        -O "samtools.tar.bz2" \
        --no-check-certificate \
        https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
    tar -jxf samtools.tar.bz2 \
        -C samtools \
        --strip-components 1
    cd samtools || exit 1
    make
    make install
    cd .. || exit 1
    rm -rf samtools.tar.bz2 samtools

    mkdir bcftools
    wget \
        -O "bcftools.tar.bz2" \
        --no-check-certificate \
        https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2
    tar -jxf bcftools.tar.bz2 \
        -C bcftools \
        --strip-components 1
    cd bcftools || exit 1
    make
    make install
    cd .. || exit 1
    rm -rf bcftools.tar.bz2 bcftools

Collection

• Name: TomHarrop/singularity-containers
• License: None

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