suujia/orca:latest

$ singularity pull shub://suujia/orca:latest

Singularity Recipe

BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

%runscript
	# print out software versions installed by linuxbrew
	find /Software/brew/Cellar -maxdepth 2 -print | sed 's|/Software/brew/Cellar||g' | sed 's|^/||' | grep "/" | sed 's|/|\t|' | sort | awk '{print $1, $2, "Homebrew"}' | column -t | sort -u --ignore-case

%post
	sed -i 's/$/ universe/' /etc/apt/sources.list
	locale-gen "en_US.UTF-8"
	dpkg-reconfigure locales
	export LANGUAGE="en_US.UTF-8"
	echo 'LANGUAGE="en_US.UTF-8"' >> /etc/default/locale
	echo 'LC_ALL="en_US.UTF-8"' >> /etc/default/locale
    echo 'linuxbrew ALL=(ALL) NOPASSWD:ALL' >>/etc/sudoers

    mkdir /Software /scratch
	chmod 777 /scratch
	chmod +t /scratch
	chmod 777 /Software

    apt-get update \
        && apt-get install -y --no-install-recommends \
                bzip2 \
                ca-certificates \
                curl \
                file \
                fonts-dejavu-core \
                g++ \
                git \
                locales \
                make \
                openssh-client \
                patch \
                sudo \
                uuid-runtime \
        && rm -rf /var/lib/apt/lists/*

	useradd -m -s /bin/bash linuxbrew
	su -c 'cd /Software && git clone https://github.com/Linuxbrew/brew.git' linuxbrew

    export HOMEBREW_NO_ANALYTICS=1 HOMEBREW_NO_AUTO_UPDATE=1 
    su -c '/Software/brew/bin/brew tap homebrew/core' linuxbrew
    rm -rf ~/.cache

    # test brew install brewsci tools 
    su -c '/Software/brew/bin/brew update' linuxbrew
    su -c '/Software/brew/bin/brew tap brewsci/bio' linuxbrew
    su -c '/Software/brew/bin/brew install \
    matplotlib \
    nextflow' linuxbrew

    sed -i 's|PATH=$PATH:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin|PATH="/Software/brew/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"|' /environment

Collection

• Name: suujia/orca
• License: GNU General Public License v3.0

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