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 (using Docker)
- Getting started (using native installation)
- 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 .
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
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 8.0)
Getting started (using Docker)
To set up a local development environment in Docker, you have to build a new Docker image for Sequencescape. start a stack of services that include a mysql database, and reset this database contents. You can do all together by running the commands:
docker-compose build RESET_DATABASE=true docker-compose up
Optionally, if this is not the first time you start the app, you may not want to reset the database, and you can run this command instead:
With this we should have started Sequencescape server and all required services. You should be able to access Sequencescape by going to http://localhost:3000 and log in with username and password admin/admin.
ABOUT LOCAL DEVELOPMENT SETUP You may want to start only the required services for Sequencescape (server and jobs worker) and use your local version of Mysql instead of the Docker version, in that case you can start this setup with the command:
docker-compose -f docker-compose-dev.yml up
ABOUT RECREATE DOCKER IMAGE If you ever need to recreate the image built on first start (because you made modifications to the Dockerfile file) you can run the building process again with:
Getting started (using native installation)
This section only applies if you don't have Docker installed or if you prefer a native installation of Sequencescape.
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/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 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 warren consumer start
The consumer will run in the foreground, logging to the console. You can stop it with Ctrl-C.
For more warren actions, either use
bundle exec warren help or see the
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 one of three ways; using rspec, via rails tests or with cucumber.
- 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
For a single file:
bundle exec ruby -Itest test/lib/label_printer/print_job_test.rb
- To run cucumber tests (found in
features/dir.) first ensure you have a
sequencescape_test_cukedatabase configured by running:
RAILS_ENV=cucumber bundle exec rake db:setup
then run cucumber itself:
bundle exec cucumber
For a single file:
bundle exec cucumber features/create_plates.feature
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
Installing on Apple Silicon (M1)
If installation issues are encountered with Docker on M1 processors, try the fixes below:
- The docker-compose build command fails with any mentions to a processor architecture ('amd64', 'x86') or the message below:
... #0 1.528 The following packages have unmet dependencies: #0 1.568 google-chrome-stable:amd64 : Depends: libasound2:amd64 (>= 1.0.17) but it is not installable #0 1.568 Depends: libatk-bridge2.0-0:amd64 (>= 2.5.3) but it is not installable ... #0 1.568 Depends: libxkbcommon0:amd64 (>= 0.5.0) but it is not installable #0 1.568 Depends: libxrandr2:amd64 but it is not installable #0 1.581 E: Unable to correct problems, you have held broken packages. ------ failed to solve: process "/bin/bash --login -c apt install -y ./google-chrome-stable_current_amd64.deb" did not complete successfully: exit code: 100
Force docker to use the an ARM image as the base with the patch below. It is also recommended to install and enable Rosetta 2.
# ./Dockerfile -FROM ruby:2.7.8-slim +FROM --platform=linux/arm64 ruby:2.7.8-slim
- The sequencescape_server container terminates with the error:
Function not implemented - Failed to initialize inotify (Errno::ENOSYS)
Use an alternative file update checker:
# ./config/environments/development.rb # Use an evented file watcher to asynchronously detect changes in source code, # routes, locales, etc. This feature depends on the listen gem. - config.file_watcher = ActiveSupport::EventedFileUpdateChecker + config.file_watcher = ActiveSupport::FileUpdateChecker
API V2 Authentication
The V2 API has had authentication checks added to it so that other applications calling the API should provide a valid key.
The key is passed by the client application via the
Keys can be generated via the Rail Console by creating new
ApiApplication records and observing the
key attribute on them.
As of the time of writing, there are three outcomes to a request made, with respect to API key submission:
- The client calls an API V2 endpoint with a valid API key in the header of the request.
- The response given has a valid status code and the body contains the requested information/confirmation.
- The client calls an API V2 endpoint with an invalid API key in the header of the request.
- The response given has status code 401 Unauthorized and contains a JSON body explaining that a valid API key must be provided for the header.
- The request is logged with the prefix "Request made with invalid API key" including information about the client and the API key used.
- The client calls an API V2 endpoint without the API key header in the request.
- The response is given as if a valid API key was provided.
- The request is logged with the prefix "Request made without an API key" including information about the client.
- The client application should be updated to use a valid API key in future.
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:
npx 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.