Hydra-Genetics Vagrant

Build script for a vagrant machine that can be used by Window/OSX user to run snakemake in combination with singularity.

Build

Dependancies

Softwares:

• VirtualBox
• Vagrant

Vagrant plugins:

vagrant plugin install vagrant-disksize

Build vagrant machine

Make sure that your ~/.ssh folder contains an id_rsa.pub file, else modify the following line (in ubuntu/Vagrantfile)

    authorize_key(config, 'root', '~/.ssh/id_rsa.pub', '~/.ssh/id_rsa.pub')

to match one of your keys.

git clone https://github.com/hydra-genetics/vagrant.git
cd vagrant/vagrant_systems/ubuntu/
vagrant up

Folder vagrant_systems/ubuntu/data/ will be mounted into the vagrant machine for easy data sharing.

Remove machine

cd vagrant_systems/ubuntu/
vagrant destroy

Enter machine

cd vagrant_systems/ubuntu/
vagrant ssh

# Liste singularity options
singulariy --help

# Install hydra-genetics
pip install hydra-genetics