galaxy

Table of Contents

1. Overview
2. Module Description - What the module does and why it is useful
3. Setup - The basics of getting started with galaxy
   • What galaxy affects
   • Setup requirements
   • Beginning with galaxy
4. Usage - Configuration options and additional functionality
5. Reference - An under-the-hood peek at what the module is doing and how

Overview

This module sets up a Galaxy server according to the specific requirements of the University of Luxembourg's HPC group and the LCSB.

So far it only works on Debian wheezy.

This is not a generally applicable puppet module that can be used as is. It contains a lot of very specific settings for the ULHPC cluster environment. Please regard it rather as a documentation of the steps to set up a production Galaxy server.

Module Description

The module sets up a Galaxy server with four load-balanced web servers and four job runners. It uses Apache2 as a proxy server and a PostGreSQL database.

Setup

What galaxy affects

• creates 'galaxy' user and group
• PostGreSQL: creates 'galaxy' and 'galaxytools' databases with user 'galaxy' as the owner
• Apache2: creates a virtual host
• /etc/init.d/galaxy
• packages: installs gcc, python, mercurial, tar and openssl

Setup Requirements

This module depends on

• puppetlabs/apache
• puppetlabs/postgresql
• puppetlabs/vcsrepo

Beginning with galaxy

For a simple standard setup just set the postgresql_password to a secure password:

class { 'galaxy':
  postgresql_password => 'securepassword',
}

Usage

It suffices to declare the galaxy class, everything else is automatically included. The $postgresql_password should definitely be changed for a production server, as well as the $id_secret. The $directory is fine with the default setting.

Reference

Class: galaxy

Does all the work.

Class: galaxy::params

This class sets the default parameters for the Galaxy puppet module.

Class: galaxy::directorystructure

This class sets up the directory structure for the project directories and mounts the galaxy project directory.

Defined Type: galaxy::projectmount

This defined resource type mounts a project directory read-only.

Limitations

Only tested on Debian wheezy.