Setup

This assumes you are building a Singularity container locally on a Mac

Make sure you've already installed Vagrant, since its needed to run Singularity on a Mac

brew cask install virtualbox
brew cask install vagrant
brew cask install vagrant-manager

If you have trouble install Vagrant with homebrew, try using this.

Creating the Container

The workflow for creating a Singularity container on a Mac through Vagrant is saved in the included Makefile.

Make the container by running:

make container

And run a test on the created container with

make test

Output

If everything worked, the following files should be created:

• singularity-vm/image/singularity-container-samtools: the Singularity container file for samtools

• singularity-vm/image/samtools-version.txt: the output from running samtools inside the container, should look like this:

samtools 1.6
Using htslib 1.6
Copyright (C) 2017 Genome Research Ltd.

Resources

http://singularity.lbl.gov/install-mac

https://app.vagrantup.com/singularityware/boxes/singularity-2.4

https://releases.hashicorp.com/vagrant/2.0.1/vagrant_2.0.1_x86_64.dmg

http://singularity.lbl.gov/docs-build-container

http://singularity.lbl.gov/docs-recipes

https://github.com/qbicsoftware/qbic-singularity-samtools