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 ===
It is strongly recommended that you use a ruby version manager such as RVM to
manage the Ruby version you are using. Sequencescape is developed using jruby-9.0.5.0
$ cp config/config.yml.example config/config.yml
$ $EDITOR config/config.yml
$ gem install bundler
$ bundle install
$ bundle exec rake db:create db:setup
# The task below is optional, but creates an admin user account and a
# few example studies and plates
$ bundle exec rake working:setup
$ bundle exec ./script/delayed_job start
$ bundle exec rails s
# 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.
$ bundle exec rake jobs:work
=== 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.
== Ruby warnings and rake 11 ==
Rake 11 enables ruby warnings by default when running the test suite. These can
be disabled with RUBYOPT='-W0', (eg. RUBYOPT='-W0' bundle exec rake test).
Currently these warnings are excessive, covering both our own code and external
dependencies. As it stands it makes the output of the test suite unusable in
travis, as it fills the buffer. These warning WILL need to be fixed, especially
in our own code.
== 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/