github.com/apptainer/singularity@v3.1.1+incompatible/examples/legacy/2.2/contrib/linuxbrew_and_non-root_software_example.def (about) 1 BootStrap: debootstrap 2 OSVersion: trusty 3 MirrorURL: http://us.archive.ubuntu.com/ubuntu/ 4 5 %runscript 6 # print out software versions installed by linuxbrew 7 find /Software/brew/Cellar -maxdepth 2 -print | sed 's|/Software/brew/Cellar||g' | sed 's|^/||' | grep "/" | sed 's|/|\t|' | sort | awk '{print $1, $2, "Homebrew"}' | column -t | sort -u --ignore-case 8 9 %post 10 sed -i 's/$/ universe/' /etc/apt/sources.list 11 locale-gen "en_US.UTF-8" 12 dpkg-reconfigure locales 13 export LANGUAGE="en_US.UTF-8" 14 echo 'LANGUAGE="en_US.UTF-8"' >> /etc/default/locale 15 echo 'LC_ALL="en_US.UTF-8"' >> /etc/default/locale 16 mkdir /Software 17 chmod 777 /tmp 18 chmod +t /tmp 19 chmod 777 /Software 20 apt-get update 21 apt-get install -y apt-transport-https build-essential cmake curl libsm6 libxrender1 libfontconfig1 wget vim git unzip python-setuptools ruby 22 apt-get clean 23 useradd -m singularity 24 su -c 'cd /Software && git clone https://github.com/Linuxbrew/brew.git' singularity 25 su -c '/Software/brew/bin/brew install bsdmainutils parallel util-linux' singularity 26 su -c '/Software/brew/bin/brew tap homebrew/science' singularity 27 su -c '/Software/brew/bin/brew install art bwa samtools' singularity 28 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