TomHarrop/variant-utils:sniffles_f958698

$ singularity pull shub://TomHarrop/variant-utils:sniffles_f958698

Singularity Recipe

Bootstrap: docker
From: ubuntu:20.04

%help
    Sniffles f958698
    https://github.com/fritzsedlazeck/Sniffles

%labels
    MAINTAINER "Tom Harrop"
    VERSION "Sniffles f958698"

%environment
    export PATH="${PATH}:/sniffles/bin/sniffles-core-1.0.12"
    export LC_ALL=C

%runscript
    exec /sniffles/bin/sniffles-core-1.0.12/sniffles "$@"

%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

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

    #############################
    # CHECK PATH ON NEW COMMITS #
    #############################
    # install Sniffles from git branch
    git clone \
        https://github.com/fritzsedlazeck/Sniffles \
        /sniffles

    (
    cd /sniffles || exit 1
    git checkout -f f958698
    git submodule update --init --recursive
    mkdir build
    cd build || exit 1
    cmake ..
    make && make install
    )

Collection


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Metrics

key value
id /containers/TomHarrop-variant-utils-sniffles_f958698
collection name TomHarrop/variant-utils
branch master
tag sniffles_f958698
commit 56857e2f4b807c5aaad56ce621e214fb7e0e9f61
version (container hash) 71a0c206aefdd1ebb6630eb08d8300c87e238794733cf83e5d62737c4906a927
build date 2020-10-05T03:06:48.095Z
size (MB) 194.74609375
size (bytes) 204206080
SIF Download URL (please use pull with shub://)
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