TomHarrop/ont-containers:minknow_20.10.3

$ singularity pull shub://TomHarrop/ont-containers:minknow_20.10.3

Singularity Recipe

Bootstrap: docker
From: ubuntu:18.04

%help
    ONT MinKNOW 20.10.3 GUI in a container

    Run as follows:

    singularity instance start \
        --nv \
        -B output/dir/run:/run,output/dir/var:/var \
        minknow_20.10.3.sif \
        minknow

%labels
    MAINTAINER "Tom Harrop"
    VERSION "MinKNOW 20.10.3"

%post
    export DEBIAN_FRONTEND=noninteractive

    # 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 update
    apt install -y \
        apt-transport-https \
        libasound2 \
        libcanberra-gtk-module \
        libcanberra-gtk3-module \
        libgconf-2-4 \
        libgtk-3-dev \
        libnss3 \
        libxss1 \
        software-properties-common \
        wget

    # install ONT repo
    export PLATFORM=$(lsb_release -cs) 
    wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub \
        | apt-key add - 
    echo \
        "deb http://mirror.oxfordnanoportal.com/apt ${PLATFORM}-stable non-free" \
        | tee /etc/apt/sources.list.d/nanoporetech.sources.list 
    apt-get update


    apt update
    apt install -y minion-nc=20.10.3-1~bionic

%startscript
    /opt/ont/minknow/bin/mk_manager_svc & /opt/ont/ui/kingfisher/MinKNOW

Collection

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

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