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galaxy

A module for a basic Galaxy installation. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

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Version information

  • 0.0.9 (latest)
  • 0.0.8
  • 0.0.7
  • 0.0.6
  • 0.0.5
  • 0.0.4
  • 0.0.3
  • 0.0.2
  • 0.0.1
released Nov 25th 2014

Start using this module

  • r10k or Code Manager
  • Bolt
  • Manual installation
  • Direct download

Add this module to your Puppetfile:

mod 'urgi-galaxy', '0.0.9'
Learn more about managing modules with a Puppetfile

Add this module to your Bolt project:

bolt module add urgi-galaxy
Learn more about using this module with an existing project

Manually install this module globally with Puppet module tool:

puppet module install urgi-galaxy --version 0.0.9

Direct download is not typically how you would use a Puppet module to manage your infrastructure, but you may want to download the module in order to inspect the code.

Download

Documentation

urgi/galaxy — version 0.0.9 Nov 25th 2014

#Galaxy ####Table of Contents

  1. Overview
  2. Module Description
  3. Usage
  4. Parameters
  5. Contact
  6. Galaxy Project

##Overview The Galaxy module allows you to download and make up a new instance of galaxy.

##Module Description This is the Galaxy module. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. This module contains the base blocks for Galaxy server configuration management. These base blocks are agregated in profiles and roles. See urgi/galaxy-roles-profiles for Galaxy roles and profiles.

##Usage ###Classes ####Class: galaxy::dependencies This class installs all the packages required to build one new Galaxy's instances: Mercurial , Python and Tar ( and Dpkg for Debian OS)

####Class: galaxy::params This class sets the default parameters for the galaxy puppet module ( create user, directory and galaxy branch)

####Class: galaxy::common_startup This class writes common_startup.sh from galaxy-central and execute it. This convert .samples files in .ini files and fetch the eggs.

####Class: galaxy::create_db This class executes create_db.sh to create a database and update it at the last version.

####Class: galaxy::manage_tools This class executes manage_tools.py wich updates the tools.

####Class: galaxy::install This class download the remote repository from bickbuckets.org/galaxy/galaxy-dist with mercurial.

####Class: galaxy::job_conf This class writes the job_conf.xml file with a template. Make sure the numbers of background workers (handlers) matches the numberwich is in galaxy_ini.pp

####Class: galaxy::service This class configures galaxy service. Currently debain/redhat are the only two supported.

####Class: galaxy::toolshed_conf This class writes Galaxy toolshed configuration. Specifies which toolsheds are available to use in the web interface.

####Class: galaxy::galaxy_ini

This class writes the galaxy.ini , the main configuration file of Galaxy.

##Parameters

See code interne documentation. All the parameters can be set by Hiera, using automatic parameter lookup : http://docs.puppetlabs.com/hiera/1/puppet.html#automatic-parameter-lookup

##Github projects

Projects for base blocks and roles+profiles are hosted on github:

https://github.com/puppet-galaxy/puppet-galaxy

https://github.com/puppet-galaxy/galaxy-roles-profiles

##Contact

Mikael Loaec mloaec@versailles.inra.fr

Olivier Inizan oinizan@versailles.inra.fr

Eric Rasche rasche.eric@yandex.ru

##Galaxy Project http://galaxyproject.org