= Installation example with a fresh Ubuntu 8.04 machine and Apache + Passenger

Although this guide is specific for Ubuntu 8.04, it can also serve as a rough guide for the steps
necessary using any operating system. There are also many other deployment choices, but Apache with
Phusion Passenger (mod_rails) is a popular one.

== Install Ruby, RubyGems, Rails

    sudo aptitude -y install ruby1.8-dev ruby1.8 ri1.8 rdoc1.8 irb1.8 libreadline-ruby1.8 libruby1.8 libopenssl-ruby sqlite3 libsqlite3-ruby1.8
    sudo ln -s /usr/bin/ruby1.8 /usr/bin/ruby
    sudo ln -s /usr/bin/ri1.8 /usr/bin/ri
    sudo ln -s /usr/bin/rdoc1.8 /usr/bin/rdoc
    sudo ln -s /usr/bin/irb1.8 /usr/bin/irb
    wget http://rubyforge.org/frs/download.php/45905/rubygems-1.3.1.tgz
    tar zxf rubygems-1.3.1.tgz
    cd rubygems-1.3.1
    sudo ruby setup.rb
    sudo ln -s /usr/bin/gem1.8 /usr/bin/gem
    sudo gem install rails

== Install MySQL and bindings for Ruby

Install MySQL server, client and client libraries:

    sudo aptitude -y install mysql-server mysql-client libmysqlclient15-dev

Choose the root password at this point. Then, install the MySQL-Ruby bindings:

    sudo aptitude -y install libmysql-ruby1.8

== Create the necessary databases

Not that I'm doing this the quick and dirty way by using the MySQL admin user, whereas if I were
going to deploy this in a production environment I would probably want to have a specific MySQL
user for SLIMseq with limited access rights.

    mysql -u root -p

At the mysql prompt:

    CREATE DATABASE slimseq_production;
    CREATE DATABASE slimseq_development;
    CREATE DATABASE slimseq_test;
    \q

== Install Subversion

    sudo aptitude -y install subversion

== Install Prerequisite Gems
sudo aptitude -y install build-essential
sudo gem install ruby-debug json parseexcel rest-client rspec-rails hpricot

== Install SLIMseq itself

    sudo mkdir /apps
    sudo chown notroot:notroot /apps
    cd /apps/
    svn co http://slimarray.systemsbiology.net/svn/branches/slimseq
    cd slimseq
    cp config/database.example config/database.yml
    vim config/database.yml

Set your username and password for the databases, comment out "socket" lines:

    rake db:load RAILS_ENV=production
    script/server -e production

If all is welll, you should be able to browse to <Server IP>:3000 and log in as admin:test

== Install Apache2 and Passenger
    sudo aptitude -y install apache2 apache2.2-common apache2-mpm-prefork apache2-utils libexpat1 ssl-cert apache2-prefork-dev
    sudo gem install passenger
    sudo passenger-install-apache2-module

Add to /etc/apache2/apache2.conf:

    LoadModule passenger_module /usr/lib/ruby/gems/1.8/gems/passenger-2.0.6/ext/apache2/mod_passenger.so
    PassengerRoot /usr/lib/ruby/gems/1.8/gems/passenger-2.0.6
    PassengerRuby /usr/bin/ruby1.8

== Configure Apache2 for SLIMseq

    sudo vim /etc/apache2/sites-available/slimseq

Add these lines:
    <VirtualHost *:80>
      ServerName www.yourhost.com
      DocumentRoot /apps/slimseq/public
    </VirtualHost>

Enable the new site you've created, disable the default one, and reload the apache configs:

    sudo a2dissite default
    sudo a2ensite slimseq
    sudo /etc/init.d/apache2 reload

Now you should be get to SLIMseq at http://www.yourhost.com