README.md
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# 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 our paper:
[Sequenceserver: A modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution (2019).](https://doi.org/10.1093/molbev/msz185)
## Installation
For installation instructions and how to use SequenceServer please see
https://sequenceserver.com/ - instructions for independently installing open-source sequenceserver are linked from the footer.
If you want to run SequenceServer directly from source code, please see
'Develop and contribute' section below.
We also offer a [hosted cloud blast service](https://sequenceserver.com) for those who prefer fully point-and-click installation and want to avoid the complexities and costs of running a server. Running the cloud service enables us to further support the development of SequenceServer.
## Referral scheme
[Refer friends or colleagues](https://sequenceserver.com/referral-program) to SequenceServer Cloud and earn up to $100 per person who signs up (as of 2023-10; exact terms may change).
## Release notes
New releases are announced on [GitHub release page](https://github.com/wurmlab/sequenceserver/releases) and on our [Support Page](https://support.sequenceserver.com).
## Reporting issues
Please report any issues here: https://github.com/wurmlab/sequenceserver/issues or on the [community support forum](https://support.sequenceserver.com)
## 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](https://www.ruby-lang.org/en/) and [RubyGems](https://rubygems.org/):
# 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](https://docs.docker.com/get-docker/), to run SequenceServer locally as a
Docker container, using the example database from the
[ncbi-blast+ debian package](https://packages.debian.org/sid/ncbi-blast+):
* Change `from final` at the end of the `Dockerfile` to `from dev`.
* Build the image with:
```bash
docker build -t sequenceserver .
```
* Run a container with...
```bash
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](https://nodejs.org/). 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](https://github.com/nektos/act) is installed
as a [GitHub CLI extension](https://github.com/nektos/act#installation-as-github-cli-extension).
Then, for instance, `.github/workflows/test.yml` would be run by:
```
gh act -j test
```
[action-validator](https://github.com/mpalmer/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
* Yannick Wurm (PI) - [email](mailto:yannickwurm@gmail.com) | https://wurmlab.com & https://sequenceserver.com
* [Mailing list / forum](https://support.sequenceserver.com)