SLIMseq¶ ↑

What is it?¶ ↑

SLIMseq is a sample tracking system for ultra-high-throughput sequencing, specifically the Illumina/Solexa platform. It is geared primarily towards a “Core Facility” model, where end users submit samples to a core facility and then the core takes care of actually running the samples on the sequencing instruments. SLIMseq captures meta data about samples as they are submitted, and then lets the core facility track the samples through being run on a flow cell, sequenced and having the Solexa pipeline run on them. Much of the sample information is available through a REST-like API.

How do I install it?¶ ↑

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 INSTALL.rdoc for details on installing these.

The prerequisites for SLIMseq are:

• Ruby version 1.8.6 or 1.8.7

• RubyGems 1.3 or higher

• Bundler 1.0 or higher

• SLIMcore (if using the SLIMcore Authorizer plugin)

• RubyCAS-server (if using the SLIMcore Authorizer plugin)

SLIMseq is a Ruby on Rails application. Those familiar with setting up Ruby on Rails applications may find the following sufficient to get it up and running (with slimcore):

git clone git://github.com/systemsbiology/slimseq.git
cd slimseq
bundle install
bin/rake setup authorizer=slimcore
script/server

For a detailed example of how to install SLIMseq on a fresh Ubuntu 8.04 machine, see the file named INSTALL.rdoc. Installation on other operating systems should be similar.

I’ve installed it, now how do I log in?¶ ↑

With the slimsolo_authorizer, you should be able to log in as user ‘admin’ with the password ‘test’.

With the slimcore_authorizer plugin, log in in as a user that will authenticate with your RubyCAS-server install. The first user to log in will automatically be made an administrator.

How do I use the API?¶ ↑

The API documentation can be reached by adding /api to the base path to your app. So if you’re hosting SLIMseq at my-server, go to my-server/api. This describes how to use the API in general as well as documenting what calls are available and what example outputs look like.