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sequencescape.sublime-project

README.md

logo Sequencescape

Build Status Maintainability Test Coverage Yard Docs

Documentation

In addition to the externally hosted YARD docs, you can also run a local server:

yard server -r --gems -m sequencescape .

You can then access the Sequencescape documentation through: http://localhost:8808/docs/sequencescape Yard will also try and document the installed gems: http://localhost:8808/docs

Description

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.

    $ cp config/aker.yml.example config/aker.yml
    $ $EDITOR config/config.yml
    $ gem install bundler
    $ bundle install
    $ bundle exec rake 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

Delayed job

For background processing Sequencescape uses delayed_job to 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

Barcode printing is carried out by a separate REST service, PrintMyBarcode. The source for this is also available on GitHub sanger/print_my_barcode

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.

Data warehousing

There is a client application for building a data warehouse based on the information in Sequencescape. This is driven asynchronously via RabbitMQ. See out various clients on GitHub:

sanger/unified_warehouse

sanger/event_warehouse

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.

NPG Software

Copyright (c) 2007, 2010-2019 Genome Research Ltd.

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