TomHarrop/assembly-utils:gffread_0.12.3

$ singularity pull shub://TomHarrop/assembly-utils:gffread_0.12.3

Singularity Recipe

Bootstrap: docker
From: ubuntu:20.04

%help
    gffread 0.12.3
    
%labels
    MAINTAINER "Tom Harrop (twharrop@gmail.com)"
    VERSION "gffread 0.12.3"

%environment
    export LC_ALL=C
    export PATH="${PATH}:/gffread"

%post
    # faster apt downloads
    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
    )

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

    # install gffread
    git clone https://github.com/gpertea/gffread /gffread
    (
    cd /gffread
    git checkout -f v0.12.3
    git submodule update --init --recursive
    make release
    )

%runscript
    exec /gffread/gffread "$@"

Collection

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

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