SequenceServer - BLAST searching made easy!
SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use.
If you use SequenceServer, please cite:
Installation
For installation instructions and how to use SequenceServer please see https://sequenceserver.com/
If you want to run SequenceServer directly from source code, please see 'Develop and contribute' section below.
Release notes
New releases are announced on GitHub release page and on our Support Page.
Reporting issues
Please report any issues here: https://github.com/wurmlab/sequenceserver/issues
Develop and contribute
To develop and contribute, you will need to run SequenceServer from source (see below).
Run SequenceServer from source code
You will need Ruby and RubyGems:
# Install bundler gem to install Ruby dependencies
gem install bundler
# Move to where you downloaded or cloned seqserv
cd sequenceserver
# Use bundler to install Ruby dependencies
bundle install
# Use bundler to run SequenceServer
bundle exec bin/sequenceserver
If you do not plan to develop, you can skip installing development dependencies
by running bundle install --without=development.
Run SequenceServer from Docker
Having installed Docker, to run SequenceServer locally as a Docker container, using the example database from the ncbi-blast+ debian package:
- Change
from finalat the end of theDockerfiletofrom dev. - Build the image with:
docker build -t sequenceserver .- Run a container with...
docker run --rm -it -p 4567:4567 sequenceserver- then select the defaults when prompted.
Otherwise, a database will need to be copied to the db volume.
Making changes to the code
During development, you should use -D option to run SequenceServer in development mode. In this mode, SequenceServer will log verbosely.
# Run SequenceServer in development mode
bundle exec bin/sequenceserver -D
If you want to modify and build frontend code, you will additionally need Node and npm. You can then run a watch server that will automatically build any changes you make the frontend code:
# Install frontend dependencies
npm install
# Run watch server to automatically build changes to the frontend code
npm run-script watch
Alternatively, you can manually build the frontend code after you have made your changes:
# Build minified JS and CSS bundles
npm run-script build
If you are using docker, you can build the frontend code and include it in the image by specifying '--target=minify' to the docker build command:
docker build . -t seqserv-with-customisations --target=minify
Testing
Ruby
We use RSpec and Capybara for testing. Our test suite covers 87% of the codebase. Tests are run automatically when you open a pull-request (see Getting code merged section below) but it may be desirable sometimes to run a single test, whole file, or all tests locally:
To run a single test (a.k.a, scenario):
bundle exec rspec spec/foo_spec.rb -e 'bar'
To run all tests in a single file:
bundle exec rspec spec/foo_spec.rb
To run all tests:
bundle exec rspec
Javascript
Unit tests for the React frontend are written using React Testing Library and jest.
One option for installing jest: npm install --save-dev jest
To run a single test :
npm run test -e "test name"
To run all tests in a single file:
npm run test file_name
To run all tests:
npm run test
Linting
We use CodeClimate for static code analysis. CodeClimate is run automatically when you open a pull-request (see Getting code merged section below) but it may be desirable sometimes to run it locally.
For this, first install CodeClimate following the instructions at https://github.com/codeclimate/codeclimate.
Once CodeClimate is installed, install the required codeclimate 'engines':
codeclimate engines:install
To run all the style checkers:
codeclimate analyze
To run eslint:
codeclimate analyze -e eslint
To run rubocop:
codeclimate analyze -e rubocop
stylelint is used for CSS:
codeclimate analyze -e stylelint
The above commands respect the respective style checker's config files, e.g., .rubocopy.yml for Rubocop and so on.
GitHub Workflows
To run workflows locally, ensure nektos/act is installed as a GitHub CLI extension.
Then, for instance, .github/workflows/test.yml would be run by:
gh act -j test
action-validator is claimed as a yaml validator for GitHub workflows.
Getting code merged
Please open a pull-request on GitHub to get code merged. Our test suite and the CodeClimate static code analysis system will be automatically run on your pull-request. These should pass for your code to be merged. If you want to add a new feature to SequenceServer, please also add tests. In addition, code should be rubocop and eslint compliant, and hard-wrapped to 80 chars per line.
If you change frontend code (JavaScript and CSS), please build (i.e., minify and compress) and commit the resulting JS and CSS bundles before opening a pull-request. This is because SequenceServer is run in production mode by the test suite.
Contact
- Anurag Priyam (architect) - email | @yeban
- Yannick Wurm (PI) - email | @yannick__
- Mailing list / forum