This project serves as a development model for EBRC's iRODS production system. The zone, resources, rules, etc. reflect a subset of EBRC's conventions. If you are more interested in just exploring iRODS in general, you should try the tutorial project at [https://github.com/mheiges/vagrant-irods_ugm2015](https://github.com/ mheiges/vagrant-irods_ugm2015).

Prerequisites

The host computer needs the following.

Vagrant

Vagrant manages the lifecycle of the virtual machine, following by the instructions in the Vagrantfile that is included with this project.

https://www.vagrantup.com/downloads.html

You should refer to Vagrant documentation and related online forums for information not covered in this document.

VirtualBox

Vagrant needs VirtualBox to host the virtual machine defined in this project's Vagrantfile. Other virtualization software (e.g. VMWare) are not compatible with this Vagrant project as it is currently configured.

https://www.virtualbox.org/wiki/Downloads

You should refer to VirtualBox documentation and related online forums for information not covered in this document.

Vagrant Librarian Puppet Plugin

This plugin downloads the Puppet module dependencies. Install the plugin with the command

vagrant plugin install vagrant-librarian-puppet

Vagrant Landrush Plugin (Optional)

The Landrush plugin for Vagrant provides a local DNS where guest hostnames are registered. This permits, for example, the rs1 guest to contact the iCAT enabled server by its ies.vm hostname - a requirement for iRODS installation and function. This plugin is not strictly required but it makes life easier than editing /etc/hosts files. This plugin has maximum benefit for OS X hosts, some benefit for Linux hosts and no benefit for Windows. Windows hosts will need to edit the hosts file.

EBRC uses a custom fork of Landrush. In an OS X terminal, run the following.

git clone https://github.com/mheiges/landrush.git
cd landrush
rake build
vagrant plugin install pkg/landrush-0.18.0.gem

If you have trouble getting the host to resolve guest hostnames through landrush try clearing the host DNS cache by running

sudo killall -HUP mDNSResponder.

You should refer to Landrush and Vagrant documentation and related online forums for information not covered in this document.

Usage

Obtain a Local Copy of This Vagrant Project

Using either Git or Subversion,

git clone https://github.com/mheiges/vagrant-irods_ebrc.git

Create hiera sensitive data file

When Vagrant first boots the virtual machine (vagrant up) it will provision iRODS software and dependencies. The provisioning is done with Puppet using parameter variables defined in puppet/environments/production/hieradata/*.yaml. Some of the parameter values are site-specific secrets that can not be committed to SCM so you will need to supply those values before running vagrant up.

In the puppet/environments/production/hieradata directory, copy sensitive.yaml.tmpl to sensitive.yaml and set values specific for your site.

Start the Virtual Machines

There are three virtual machines defined

ies: iCAT enabled resource server with iCommands. This VM alone is sufficient for working with the default ebrcResc resource.
rs1: a resource server with iCommands.
client: a server with only iCommands installed.

cd vagrant-irods_ebrc vagrant up

Or start them individually, but be aware that rs1 depends on the availability of the iCAT on ies.

vagrant up ies
vagrant up rs1
vagrant up client

ssh to the Virtual Machines

To connect to the individual VMs as the vagrant user, run one of the following.

vagrant ssh ies
vagrant ssh rs1
vagrant ssh client

iRODS Puppet module development

The Vagrantfile calls Puppet librarian to assemble the required modules in puppet/modules as one of the provisioning steps. Librarian deletes and repopulates puppet/modules with each provisioning, removing any development edits you might have made. To disable the Puppet librarian module management, create the file nolibrarian in the same directory as Vagrantfile.

Limitations

Dependency on EBRC Yum Repository

The iRODS software provisioning depends on EBRC's private yum repository. You will need to be within EBRC's IP subnets in order to do the provisioning. Once the virtual machines are provisioned you can work with them anywhere. This dependency on the restricted yum repo will be removed if and when RENCI establishes their public repository as part of the iRODS 4.2 release.

Preference for Landrush Plugin and OS X

The installation of the resource server (rs1) depends on the ies.irods.vm hostname being resolvable to the IP address of the iCAT-enabled-server (ies).

The landrush plugin provides a DNS infrastructure that includes entries each of the guests. With this DNS in place, a single vagrant up command will sequentially and seamlessly prepare each ies, rs1 and client guest. That is, by the time rs1 needs to talk to the IES server, ies.irods.vm will be configured and resolvable in DNS. This infrastructure is best supported on OS X and not at all on Windows hosts. See the landrush documentation for further explanation.

With out the DNS provided by the landrush plugin you will need to vagrant up --no-provision each box separately, manually cross-reference the guests in /etc/hosts files and then manually provision with Puppet in ies, rs1, client order (see Manual iRODS Installation in this document).

Manual iRODS Installation

sudo /opt/puppetlabs/bin/puppet apply --environment=production /etc/puppetlabs/code/environments/production/manifests/site.pp

Packaging `ies` node for application development

This Vagrant project is targeted for development of Puppet manifests and advanced tinkering with iRODS feature. For a lot of application development one only needs the ies box to provide the data ingress/egress over the default resource. To support that, the ies box alone can be packaged for distribution. See https://github.com/EuPathDB/vagrant-irods_ebrc_prod_model.git for example Vagrant project.

cd vagrant-irods_ebrc

rm irods-ebrc-prod-model.box

vagrant package --base $(cat .vagrant/machines/ies/virtualbox/id) --output irods-ebrc-prod-model.box

SHA2=(`shasum -a 256 irods-ebrc-prod-model.box`)

Lookup the current version in the json file.

jq '.versions[-1].version' irods-ebrc-prod-model.json
"1.0.0"

Pick a desired incremented value and update the json file.

VER=1.0.1

Append an entry for this new version in the webdev.json file.

jq --arg ver $VER --arg sha2 $SHA2 '.versions += ( [{
  "providers": [
    {
      "checksum": $sha2,
      "checksum_type": "sha256",
      "name": "virtualbox",
      "url": "http://software.apidb.org/vagrant/irods-ebrc-prod-model/\($ver)/irods-ebrc-prod-model.box"
    }
  ],
  "version": $ver
}
] )' irods-ebrc-prod-model.json | sponge irods-ebrc-prod-model.json

Create a directory on the webserver

ssh luffa.gacrc.uga.edu "mkdir /var/www/software.apidb.org/vagrant/irods-ebrc-prod-model/${VER}"

Uploade the box, to versioned directory, and json file, to web root directory.

rsync -aPv irods-ebrc-prod-model.json luffa.gacrc.uga.edu:/var/www/software.apidb.org/vagrant/

rsync -aPv irods-ebrc-prod-model.box \
    luffa.gacrc.uga.edu:/var/www/software.apidb.org/vagrant/irods-ebrc-prod-model/${VER}

VEuPathDB/vagrant-irods_ebrc