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 over 5 million samples and 1.8 million pieces of labware and is used in a organisation of 900 people.
- Getting started
- Linting and formatting
- 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
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
Sequencescape has its own message broker and consumer. To develop this or run it locally, you must have RabbitMQ installed. It may be easiest to use the docker image (https://hub.docker.com/_/rabbitmq).
docker run -d --hostname my-rabbit --name some-rabbit -p 8080:15672 -p 5672:5672 rabbitmq:3-management
It can be useful to follow the rabbitmq logs, to look for broken connections or other problems. To do this using the docker image,
get the container id using
docker ps, and then:
docker logs -f <container id>
To start the consumer off listening for messages:
bundle exec ./bin/amqp_client start
start instructs it to start. You can also stop a worker by calling
or restart it with
Logs can be found in
You will also have to change the config in config/warren.yml from
type: log to
type: broadcast to get
it to actually send messages in development mode.
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
Linting and formatting
Rubocop is used for linting.
bundle exec rubocop
Prettier is used for formatting.
yarn prettier --check . yarn prettier --write .
- Prettier rules are configured in .prettierrc.json
- Whole files can be ignored in .prettierignore
- Sections of files can be disabled using #prettier-ignore
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 our various clients on GitHub:
Lefthook is a git-hook manager that will ensure staged files are linted before committing.
You can install it either via homebrew
brew install Arkweid/lefthook/lefthook or rubygems
gem install lefthook
You'll then need to initialize it for each repository you wish to track
Hooks will run automatically on commit, but you can test them with:
lefthook run pre-commit
In addition you can also run
lefthook run fix to run the auto-fixers on staged files only.
Note that after doing this you will still need to stage the fixes before committing. I'd love to be
able to automate this, but haven't discovered a solution that maintains the ability to partially
stage a file, and doesn't involve running the linters directly on files in the .git folder.
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 GH actions builds use the Knapsack-pro gem to reduce build time by parallelizing the RSpec and Cucumber tests. There is no need to regenerate the knapsack_rspec_report.json file, Knapsack Pro will dynamically allocate tests to ensure tests finish as close together as possible.
Copyright (c) 2007, 2010-2021 Genome Research Ltd.