hurwitzlab/imicrobe-vm

Name: imicrobe-vm

Owner: Hurwitz Lab

Description: Scripts to provision a VM to run iMicrobe.

Created: 2017-03-13 12:17:26.0

Updated: 2017-07-25 19:39:20.0

Pushed: 2018-01-03 20:24:50.0

Homepage: null

Size: 79

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

imicrobe-vm

Scripts to build and provision a VM running iMicrobe.

Requirements

Building a VM with these scripts requires Vagrant, VirtualBox, and Ansible. Installing Vagrant and VirtualBox will not be described here. Steps to install Ansible are given below.

In addition the Ansible script relies on the following roles available from ansible-galaxy:

• CSCfi.mariadb
• lesmyrmidons.mongodb

Instructions for installing these roles are given below.

It is recommended that Ansible be installed in a Python 3.6+ virtual environment. If a Python 3.6+ interpreter is available then a virtual environment can be created like this:

thon3 -m venv ~/venv/imicrobevm
urce ~/venv/imicrobevm/bin/activate
crobevm)$ pip install ansible
crobevm)$ ansible-galaxy install -r ansible.galaxy.roles.yml

If a Python 3.6+ interpreter is not already available then a convenient method to install one is with Miniconda3.

After installing Miniconda3 create a virtual environment and install Ansible like this:

nda create python=3.6 --name imicrobevm
urce activate imicrobevm
crobevm)$ pip install ansible
crobevm)$ ansible-galaxy install -p ~/etc/ansible/roles -r ansible.galaxy.roles.yml

Install vagrant-vbguest plugin

It is very helpful but not necessary to install the vagrant-vbguest plugin. This Vagrant plugin automatically installs the correct version of VirtualBox Guest Additions kernel modules in a VM after VirtualBox is updated. Install the plugin with this command:

grant plugin install vagrant-vbguest

Installation

Clone the repository

t clone https://github.com/hurwitzlab/imicrobe-vm.git

Make a local copy of Vagrantfile.default and customize it for your host

Add directories to be shared, set up port forwarding, set the number of CPUs and amount of memory the VM will use, and more!

 Vagrantfile.default Vagrantfile

Make a local copy of imicrobe_vars.yml.default and enter the necessary information

 imicrobe-vm
 imicrobe_vars.yml.default imicrobe_vars.yml

Build an iMicrobe Virtual Machine

urce activate imicrobevm
crobevm)$ vagrant up

Restart Nginx

Log in to the VM and restart Nginx.

grant ssh
ant@vagrant:~$ sudo systemctl restart nginx

Development

Access to the server is available through https://localhost:8443/.