TomHarrop/align-utils:minimap2_2.17r941

$ singularity pull shub://TomHarrop/align-utils:minimap2_2.17r941

Singularity Recipe

Bootstrap: docker
From: ubuntu:20.04

%help
    minimap2 2.17 (r941)
    
%labels
    MAINTAINER "Tom Harrop (twharrop@gmail.com)"
    VERSION "minimap2 2.17 (r941)"

%environment
    export LC_ALL=C
    
%post
    export DEBIAN_FRONTEND=noninteractive
    export LC_ALL=C

    # reset apt
    apt-get clean
    rm -r /var/lib/apt/lists/*
    (
        . /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-get update
    apt-get upgrade -y --fix-missing

    # install dependencies
    apt-get install -y \
        build-essential wget zlib1g-dev

    # install k8
    wget -O "/k8.tar.gz" \
        --no-check-certificate \
        https://github.com/attractivechaos/k8/releases/download/0.2.5/k8-0.2.5.tar.bz2
    mkdir /k8
    tar -xjf /k8.tar.gz \
        -C /k8 \
        --strip-components 1
    mv /k8/k8-Linux /usr/local/bin/k8
    rm -r /k8 /k8.tar.gz

    # install minimap2
    wget -O "minimap2.tar.gz" \
        --no-check-certificate \
        https://github.com/lh3/minimap2/archive/v2.17.tar.gz
    mkdir minimap2
    tar -zxf minimap2.tar.gz \
        -C minimap2 \
        --strip-components 1

    cd minimap2 || exit 1
    make
    mv minimap2 /usr/local/bin/
    mv misc/paftools.js /usr/local/bin/

    cd .. || exit 1
    rm -rf minimap2 minimap2.tar.gz

%runscript
    exec /usr/local/bin/minimap2 "$@"

Collection

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

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