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Installation example with a fresh Ubuntu 8.04 machine and SQLite3 + 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. SQLite3 is used here for the sake of simplicity, but MySQL will probably be a better choice for a production environment, and can easily be used by configuring it in the config/database.yml. SLIMcore Authorizer is the default since this is what’s being used at Institute for Systems Biology where SLIMseq was developed.

Prerequisites ↑

SLIMseq can be installed either as a standalone application, or using shared infrastructure that allows single sign-on and shared users and lab groups with other applications such as SLIMarray. The shared infrastructure install requires that you separately install SLIMcore (github.com/systemsbiology/slimcore/tree/master) and RubyCAS-server (github.com/gunark/rubycas-server/tree/master).

See the “Install Extras for SLIMcore Authorizer” at the end of this document for details on installing SLIMcore and RubyCAS-server/RubyCAS-client.

Install Ruby, RubyGems, Rails and Rake ↑

sudo aptitude update && sudo aptitude upgrade
sudo aptitude -y install ruby1.8-dev ruby1.8 ri1.8 rdoc1.8 irb1.8 libreadline-ruby1.8 libruby1.8 libopenssl-ruby libmysql-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 -v=2.2.2
sudo gem install rake

Install Git ↑

sudo aptitude -y install git-core

Install Prerequisites For Gems ↑

sudo aptitude -y install build-essential
sudo aptitude -y install libxml2-dev libxslt1-dev

Install SLIMseq itself ↑

sudo mkdir /apps
sudo chown notroot:notroot /apps
cd /apps/
git clone git://github.com/systemsbiology/slimseq.git
cd slimseq

Run the setup task ↑

Running the setup task will install the necessary plugins and gems, initialize the database and create and administrator user. This needs to be run using sudo since it will be installing some gems.

# using authorizer=slimsolo here will cause the setup task to instead us slimsolo_authorizer
sudo rake setup authorizer=slimcore

Run the server ↑

script/server

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

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 the provided lines to /etc/apache2/apache2.conf.

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 www.yourhost.com

Install Extras for SLIMcore Authorizer ↑

SLIMcore Install Instructions (only needed with SLIMcore Authorizer) ↑

Follow the documentation at github.com/systemsbiology/slimcore/tree/master.

RubyCAS Install Instructions (only needed with SLIMcore Authorizer) ↑

RubyCAS-server depends upon the Picnic gem, however there’s an issue with Picnic and newer versions of Passenger. This is problematic since SLIMcore uses Rails 2.3.2, which requires Passenger 2.1+. When installing RubyCAS-server, be sure to install the following forks of Picnic and RubyCAS-server:

sudo gem sources -a http://gems.github.com
sudo gem install systemsbiology-picnic -v=0.8.0.20090421

Also install the gettext gem:

sudo gem install gettext

Then, install RubyCAS-server from this source:

git clone git://github.com/systemsbiology/rubycas-server.git /apps/rubycas-server
cd /apps/rubycas-server
cp config.example.yml config.yml
# edit setting in config.yml
mkdir public tmp

Assuming an Apache and Passenger installation as decribed above, do:

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

Add these lines:

<VirtualHost *:3030>
  ServerName www.yourhost.com
  DocumentRoot /apps/rubycas-server/public
</VirtualHost>

Enable the new site you’ve created and reload the apache configs:

sudo a2ensite rubycas
sudo /etc/init.d/apache2 reload

Finally, install the RubyCAS-client gem:

sudo gem install gunark-rubycas-client