Local Setup

Install Singularity

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

Assuming you are using a Mac;

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

Vagrant had issues installing, can also use this one:

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

Setup Vagrant Singularity VM

Start the Vagrant VM and ssh into it

mkdir singularity-vm
cd singularity-vm

vagrant init singularityware/singularity-2.4
vagrant up
vagrant ssh

Creating the Container

Build the included samtools recipe

git clone https://github.com/stevekm/singularity-samtools-demo.git

cd singularity-samtools-demo

sudo singularity build singularity-container-samtools Singularity

Running the Container Application

singularity exec singularity-container-samtools samtools --version
# samtools 1.6
# Using htslib 1.6
# Copyright (C) 2017 Genome Research Ltd.

singularity exec singularity-container-samtools samtools view input/HapMap-B17-1267.bam

Notes

Need to figure out how to deal with binding paths...

singularity exec singularity-container-bwa bwa mem -M -v 1 ./hg19_genome.fa NGS580-demo-data/fastq/HapMap-B17-1267_S8_L001_R1_001.fastq.gz NGS580-demo-data/fastq/HapMap-B17-1267_S8_L001_R2_001.fastq.gz
 singularity shell -B /data:./ singularity-container-bwa

Resources

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

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

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

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

some container collections here

https://singularity-hub.org/u/apeltzer

https://singularity-hub.org/collections/93