galaxy_roles_profiles

Contains roles and profiles for a Galaxy server management.

Module Stats

12,125 downloads

9,614 latest version

0.1 quality score

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Version information

released Nov 25th 2014

Start using this module

Installation method

Add this module to your Puppetfile:

mod 'urgi-galaxy_roles_profiles', '1.1.1'

Learn more about managing modules with a Puppetfile

Add this module to your Bolt project:

bolt module add urgi-galaxy_roles_profiles

Learn more about using this module with an existing project

Manually install this module globally with Puppet module tool:

puppet module install urgi-galaxy_roles_profiles --version 1.1.1

Tags: debian, centos, galaxy, bioinformatics, galaxy-roles-profiles

Documentation

urgi/galaxy_roles_profiles — version 1.1.1 Nov 25th 2014

#Galaxy roles profiles ####Tables of Contents

Overview
Module Description
Setup
- First step with Galaxy Roles Profiles
Usage - The classes,roles and profiles available for configuration
Deal with Hiera configuration files
Github Projects
Contacts
Galaxy Project

##Overview This module install and configure a new instance of Galaxy. Today, there are three roles (three configuration) you can choose.

##Module Description This is the galaxy-roles-profiles module. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. This module contains roles and profiles for a Galaxy server configuration management. It uses base blocks hosted in the Galaxy module: https://forge.puppetlabs.com/urgi/galaxy

##Setup what this module affect:

Create a new user, galaxy
Create directories
Manage configurations files
Enable apache
see https://forge.puppetlabs.com/puppetlabs/apache for further information

###First step Download from the Puppet Forge : https://forge.puppetlabs.com/urgi/galaxy_roles_profiles.

Configure Hiera. (See 6.Deal with Hiera).

How to install existing role: -In a file.pp

    include galaxy-roles-profiles::role::<the role wich you want>

-In the terminal

    puppet apply -e "include galaxy-roles-profiles::role::<the role wich you want>"

##Usage ###Classes ###Roles Roles contains only one or many profiles.

####Role: galaxy_roles_profiles::role::galaxy-sqlite Galaxy with SQLite.

    puppet apply -e "include galaxy_roles_profiles::role::galaxy-sqlite"

####Role galaxy_roles_profiles::role::galaxy-postgresql Galaxy with PostgreSQL

    puppet apply -e "include galaxy_roles_profiles::role::galaxy-postgresql"

####Role: galaxy_roles_profiles::role::galaxy-apache-sqlite Galaxy with SQLite and Apache.

    puppet apply -e "include galaxy-roles-profiles::role::galaxy-apache-sqlite"

####Role: galaxy_roles_profiles::role::galaxy-apache-postgresql Galaxy with PostgreSQL and Apache.

    puppet apply -e "include galaxy_roles_profiles::role::galaxy-apache-sqlite-postgresql"

###Profiles Profiles contains one or many building-block (for example galaxy::galaxy_ini). One profile is one technology layer.

####Profile: galaxy_roles_profiles::profile::sqlite This profile call galaxy::create_db.

####Profile: galaxy_roles_profiles::profile::common This profile install Galaxy using base blocks from urgi/galaxy module. This profile manage toolshed_conf, job_conf and galaxy.ini. You can change your config using Hiera and write in .yaml what you want.

####Profile: galaxy_roles_profiles::profile::postgresql This profile install packages for postgresql, and configure it for add a new database for galaxy. This uses the puppetlabs/postgresql module. These are set in a Hiera file. ( see 6.Hiera ). Further information available at : https://forge.puppetlabs.com/puppetlabs/postgresql .

####Profile: galaxy_roles_profiles::profile::apache This profile install and configure apache to deal with Galaxy. This uses puppetlabs/apache module to install apache, create a Virtual Host and load the needed mods To deal with balancer configuration file, we write a template ( balancer_galaxy.conf.erb ) and a class galaxy-roles-profiles::balancer-config Further information available at : https://forge.puppetlabs.com/puppetlabs/apache .

####Profile: galaxy_roles_profiles::profile::galaxy This profile call galaxy::service to start galaxy as service.

##Hiera First you have to edit the hiera.yaml in /etc/hiera.yaml and in /etc/puppet/hiera.yaml (for example delete each lines in hierarchy and add "common" ).

Next you have to have one hiera file in /var/lib/hiera/ ( for example common.yaml)

You can use a sample of common.yaml and modify it as you want :

$ cp /etc/puppet/modules/galaxy_roles_profiles/examples/common.yaml /var/lib/hiera -> if you have install the module.

$ cp ../galaxy_roles_profiles/examples/common.yaml /var/lib/hiera -> if you use the repo from GitHub directly.

More details on Hiera at : http://docs.puppetlabs.com/hiera/1/

More details on 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