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#Welcome to The Metric Tracker

Metric Tracker is a Ruby on Rails application for displaying and interacting with data from mass spec proteomics experiments.

##Installation Read below about the dependencies. To facilitate the process, I've generated a script which should help automate some of the process. First, you will definitely need to install Ruby (step 1 below). If you've done that then you can use git (step #2 below) to copy the repository to a local directory by running git clone git://github.com/princelab/metriculator.git . Once that is done, you can run ./bin/archiver-install to run the automated installer. Do this for each computer on which you'll be using archiver.

###Dependencies

  1. Ruby 1.9: The installation process assumes you have a working Ruby installation of at least version 1.9.

     ruby --version

    If you need help installing Ruby, see the Ruby home page. We recommend RVM as the installation option if it is available for your platform, but pick the one that seems best to you.

  2. You should install git. Git for windows can be found here: Git for Windows.

  3. You also need a working RubyGems installation, and the bundler gem installed.

     gem install bundler

  4. The SQLite database. You may already have it installed, so check before installing it again.

Automated Installation (RECOMMENDED)

Check out the project from git, and install the required gems:

git clone https://github.com/princelab/metriculator.git 
cd metriculator

Then try the automated configuration and installation tool:

./bin/archiver-install

Configuring the Thermo Scientific Xcalibur hook

Once you have installed Metriculator as a data acquisition utility on a computer which performs data acquisition, we can configure it to automatically archive your files, and kick off other downstream analysis (metric generation, and other hooks like discussed in the section, Custom Integrators.
The hook script is called ruby_caller.bat and can be found in the root directory. Call it from the method to be called after run acquisition box in Xcalibur run configuration and it will go to work when your run is completed.

###Installing The Metric Tracker Manually

Check out the project and install the required Gems:

 git checkout git://github.com/princelab/metriculator.git %% cd metriculator
 bundle install # this sets up the required libraries for running the site

This will require the installation of a dev-kit when running in windows. Fortunately, there are instructions provided when bundle install fails. When that has been done, bundle install again.

Now you need to set up the database configuration via the database.yml file. There is an example file in config/database.yml.example.

  cp config/database.yml.example config/database.yml

You need to edit the config/database.yml file so the database paths point to where you want your databases to be stored. We'd recommend making the file in the shared storage location if you are running a distributed system. The file has <%ChangeThisVariableBlock %> where you need to providhttp://www.modrails.com/documentation/Users%20guide%20Apache.htmle a valid path. The file does not need to exist yet, but the folder the file will be in does need to exist. For example, my development database on line 9 of the file reads: database: /Users/jergason/Dropbox/prince_lab_stuff/metriculator/db/metrics_site_test.db. You'll only really need the production database unless you plan on developing.

Now we set up the database:

 bundle exec rake db:automigrate

Unfortunately, the webserver aspect of this will also require some effort, at least for the best user experience possible. To that end, it should be achievable by following the directions that are given when you run:

 gem install passenger

and

 passenger-install-apache2-module

[Source: http://www.modrails.com/install.html ]

##Running The Metric Tracker

Start the server of choice. If you want to use the built-in server that comes with Rails, run:

 bundle exec rails s

Now go to http://localhost:3000 to see the site in action.

However, if you are configuring it for a more permanent (and faster) use, than you should use the passenger-apache method mentioned above. Apache is somewhat challenging to configure, and I am hardly an expert, but have figured it out with Google searches before. However, my situation was more complex, and you will likely have few problems with a simple installation. Passenger has instructions on how to integrate with apache at Passenger users guide, Apache edition.

Custom Integrators

Metriculator provides a framework for integrating your own plugins and utilities to set points within the architecture. Additional integration set points can be configured, and we would welcome pull-requests to accomplish those.

As way of example, you can read in submit_to_xtandem_example.rb

The current integration points are

    [:on_db_store, :on_finish, :on_parse]

#LICENSE Released under the MIT license, as referenced in LICENSE

#Parting words Above all, if you have problems, feel free to contact me via github, preferably after submitting an issue on github. Thanks!