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
- 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 samples and 1.3 million pieces of labware and is used in a organisation of 900 people.
- Getting started
- Rake tasks
- Supporting applications
In addition to the externally hosted YARD docs, you can also run a local server:
yard server -r --gems -m sequencescape .
The following tools are required for development:
- ruby (version defined in the
- node (version defined in the
- mysql client libraries - if you do not want to install mysql server on your machine, consider
brew install mysql-client. Alternatively, to install the MySQL required by Sequencescape (currently 5.7) use this helpful link.
It is strongly recommended that you use a ruby version manager such as RVM or rbenv to manage the
Ruby version you are using. The ruby version required should be found in
If you have the rbenv ruby-build plugin it is as simple as:
It will pick up the version from the .ruby-version file automatically
Automatic Sequencescape setup
To automatically install the required gems, set-up default configuration files, and set up your database run:
Manual Sequencescape setup
In the event you have trouble with the automatic process, you may wish to step through the various steps manually.
Bundler is used to install the required gems:
gem install bundler bundle install
If you experience
An error occurred while installing ruby-oci8 then disable the oracle gem installation:
bundle config without warehouse
The oracle adapters are not needed for development.
config/aker.example.yml file to
config/database.yml file saves the list of databases.
Create the database tables
bundle exec rake db:setup
Install webpacker and the required JS libraries
bundle exec rails webpacker:install
bundle exec rails s
Once setup, the default user/password is
For background processing Sequencescape uses
delayed_job to ensure that the server is running. It
is strongly recommended to start one for Sequencescape to behave as expected.
bundle exec rake jobs:work
bundle exec ./script/delayed_job start
Testing is done in three ways; using rspec, rails test and feature tests.
To run the rspec tests (found in
bundle exec rspec --fail-fast [<path_to_spec>]
To run the rails tests (found in
bundle exec rake test -f
Rake tasks are available for specialised tasks as well as support tasks. Support tasks allow ease of running standalone scripts multiple times.
A breakdown of the the available tasks and how to run them can be found here
There are a number of services that are needed in certain parts of Sequencescape these are listed below.
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 you are required to use a webservice for supplying numbers for plates with a simple service.
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:
Ruby warnings and rake 11
Rake 11 enables ruby warnings by default when running the test suite. These can be disabled with
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 warnings 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.
MySQL errors when installing
If you are using homebrew with rbenv and run into errors relating to SSL, have a look here
Updating the table of contents
To update the table of contents after adding things to this README you can use the markdown-toc node module. To install it, make sure you have install the dev dependencies from yarn. To update the table of contents, run:
yarn markdown-toc -i README.md --bullets "*"
The Travis builds use the Knapsack gem to reduce build time by parallelizing the RSpec and Cucumber tests. When a Travis build runs, Knapsack uses the knapsack_rspec_report.json and knapsack_cucumber_report.json files, which list out test run times, to split the tests into equal length jobs. These report files don't need to be regenerated if tests are deleted or added unless the tests in question are particularly slow and will therefore impact the build times significantly. To regenerate a report file, run one of the following, and commit the resulting changes to the report files:
KNAPSACK_GENERATE_REPORT=true bundle exec rspec KNAPSACK_GENERATE_REPORT=true bundle exec cucumber
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