VirtualBox

A VirtualBox virtual machine is provided for running SNVPhyl along with Galaxy. This machine requires at least 4 GB of memory and 4 CPUs to properly run. The machine can be quickly launched using Vagrant with the following commands.

git clone https://github.com/phac-nml/snvphyl-galaxy
cd snvphyl-galaxy/vagrant
vagrant up

Running vagrant up will download and launch the virtual machine. Galaxy can be accessed by navigating to http://localhost:48888. The default username and passwords are:

  • User: admin@localhost.localdomain
  • Password: adminpassword

Once logged in, the workflows for SNVPhyl can be accessed by clicking on Workflow at the top.

Accessing the Virtual Machine

SSH access to the machine is provided by running:

vagrant ssh

Or, alternatively, by running:

ssh -p 2222 vagrant@localhost

The vagrant user has a password of vagrant and is configured for sudo access. The Galaxy installation directory is /home/galaxy and log files can be monitored by running tail -f /home/galaxy/galaxy/paster.log.

Managing the Virtual Machine

The virtual machine can be shutdown by running (from the host machine):

vagrant halt

The virtual machine instance can be deleted by running:

vagrant destroy

VirtualBox Import

As an alternative to Vagrant, a VirtualBox image can be downloaded and imported from https://irida.corefacility.ca/downloads/snvphyl-galaxy/snvphyl-galaxy-current.zip.

Building Custom Virtual Machines

The SNVPhyl Galaxy VM is built using Packer. This can be customized or re-built by following the instructions at https://github.com/phac-nml/snvphyl-galaxy/tree/master/packer.