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README

Sequencescape is a cloud based and highly extensible LIMS system for use in labs with
large numbers of samples. 
 
 * Work order tracking
 * Sample and study management
 * Capacity management for pipelines
 * Accounting
 * Accessioning for samples and studies at the EBI ENA/EGA
 * Dynamically defined workflows for labs with support for custom processes
 * Labware and freezer tracking
 * API support for 3rd party applications

Current installation supports a million sampled and 1.3 million pieces
of labware and is used in a organisation of 900 people. 

=== Getting started ===

$ cp config/config.yml.example config/config.yml
$ $EDITOR config/config.yml
$ gem install bundler
$ bundle install
$ bundle exec rake db:schema:load
$ bundle exec rake db:seed
$ bundle exec ./script/delayed_job start
$ bundle exec ./script/server
# Login as admin/admin

=== Data model ===

 +--------+
 | Sample |                     +-------+
 +--------+                   _ | Study |
     |                      /   +-------+
 +-------+     +---------+ /    +---------+
 | Asset | --- | Request | -----| Project |
 +-------+     +---------+      +---------+

== Delayed job ==

For background processing Sequencescape uses delayed_job ensure
that the server is running.

=== Supporting applications ===

There are a number of services that are needed in certain parts
of Sequencescape these are listed bellow.

== Barcode printing ==

Sequencescape expects a barcode printing SOAP service to run
on the given URL. The WSDL of the service is defined in
doc/barcode.wsdl. We will in the future work on extracting
our barcoding Hitachi Printing Language generator. Which
we use for barcode printing.

== Plate barcode service ==

Due to DNA plate barcode series being stored in a legacy system
in Sanger your required to use a webservice for supplying numbers 
for plates with a simple service.

== Barcode rendering (danio) ==

To render barcodes you need the danio application. It will generate
an image from a barcode.

== Pico green ==

To analyse Pico green plats you need for the pico green application.

== Data warehousing ==

There is a client application for building a data warehouse based
on the information in Sequencescape.

== NPG - Illumina tracking software ==

For tracking illumina instruments you need the NPG systems.
NPG is linked to Sequencescape via a cluster formation batch
which represents a flowcell.

http://www.sanger.ac.uk/resources/software/npg/


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