bactopia-baseline

A small vagrant VM to provide a baseline for running and testing the bactopia pipeline.

Requirements

• Vagrant
• Virtual Box
• vagrant-vbguest (vagrant plugin install vagrant-vbguest)
• 50gb of available storage
• 8gb of available RAM
• 4 available CPU cores

Running

1. Use the following command to start up the vagrant VM from the root of this repository.

   vagrant up

2. ssh into the new VM and execute the run-bactopia-local.sh script as root inside of a login shell to load anaconda and the bactopia environment

   vagrant ssh
   sudo bash -l -c /home/vagrant/run-bactopia-local.sh

Useful Vagrant Commands

Start the VM

vagrant up

Shutdown the VM

vagrant halt

Destroy the VM

vagrant destroy

VM Status

vagrant status