Beta version: GitHub Master:

SequenceServer - BLAST searching made easy!

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for personal or group use.

Version 1.0.11

• Stable release
• Release date: June 2017
• Works with BLAST 2.2.30

For installation instructions and how to use SequenceServer please see http://sequenceserver.com.

If you want to install and use SequenceServer from source, we recommend the use of 'bundler' Ruby gem to install dependencies and to run SequenceServer:

# Install bundler gem
gem install bundler

# Use bundler to install dependencies
cd sequenceserver
bundle install --without=development

# Use bundler command to run SequenceServer
bundle exec bin/sequenceserver

If you use SequenceServer, please cite our preprint:

Priyam A, Woodcroft BJ, Rai V, Munagala A, Moghul I, Ter F, Gibbins MA, Moon H, Leonard G, Rumpf W & Wurm Y. 2015. Sequenceserver: A modern graphical user interface for custom BLAST databases. biorxiv doi: 10.1101/033142.

Version 1.1.0-beta12

This is a beta release of SequenceServer 2.0

Here, we have changed the underlying architecture to persist jobs so that the results can be bookmarked or shared, and to support integration with grid engines such as qsub. Furthermore, the HTML report is now generated in the browser by fetching BLAST results in JSON format from the server. This facilitates the use of existing JavaScript libraries to visualise BLAST results.

The new beta releases are announced on Google Group and on the GitHub release page.

Install and configure

To get the latest 1.1.0-beta release, run:

gem install --pre sequenceserver

If you are new to the above command, please consult the 'Install or update' section on our website http://sequenceserver.com.

If you want to install and use the beta versions from source, the process is the same as for the old stable release (instructions above).

Develop and contribute

In addition to Ruby and RubyGems, you will need Node and npm if you want to build JavaScript assets, and CodeClimate to run static code analysis.

If you want to submit a pull-request, you don't need to build JavaScript assets (we will do it) or to have run CodeClimate.

To develop and contribute, you will need to run SequenceServer from source (see previous section).

Workflow commands

Launch SequenceServer in development mode. In development mode SequenceServer logs verbosely and uses raw front-end files.

bundle exec bin/sequenceserver -D

Run tests:

bundle exec rspec

Run code style checkers (rubocop, csslint, eslint) -

codeclimate analyze

To install JS dependencies to be build JS and CSS bundles:

npm install

Build minified JS and CSS bundles:

npm run-script build

Docker builds

Both the old stable and new beta versions of SequenceServer are available as Docker images.

# With database fasta files inside a folder named db
docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver

This will use the new beta release of SequenceServer. To use the old stable release, add the version tag to the command:

# With database fasta files inside a folder named db
docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver:1.0.11

Contact

• Anurag Priyam (architect) - email | @yeban
• Yannick Wurm (PI) - email | @yannick__
• Mailing list / forum

Big Thanks

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