= 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 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 Rails itself already installed):

    gem install ruby-debug json parseexcel rest-client rspec-rails hpricot
    svn co http://slimarray.systemsbiology.net/svn/branches/slimseq
    rake db:load
    script/server

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

== I've installed it, now how do I log in?

Log in as the initial administrator user using:

Login: admin
Password: test

== 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 http://my-server, go to http://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.