SequenceServer - BLAST searching made easy!
SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
Please cite: 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.
Install and configure
Please see http://sequenceserver.com.
Develop and contribute
You will need Ruby and RubyGems, Node and npm, and CodeClimate. Further, please
1.0.x branch contains the stable releases, while the
branch is a work in progress towards next release and may be buggy.
Get source code and install dependencies.
git clone https://github.com/wurmlab/sequenceserver gem install bundler cd sequenceserver npm install bundle
We use Capybara with WebKit driver for functional testing, which requires
to be installed. If
bundle fails, install
qt (On Mac:
brew install qt)
If you are deploying SequenceServer from git you can skip
npm install step
and skip installing gems used for testing (and
qt), etc. by running:
bundle install --without=development
Run, test, build
Launch SequenceServer in development mode. In development mode SequenceServer logs verbosely and uses raw front-end files.
bundle exec bin/sequenceserver -D
Run the specs, lint the code, build front-end and package everything as a gem.
Sometimes you may just want to run the specs or lint the code:
rake spec rake lint
# With database fasta files inside a folder named db docker run --rm -ti -p 4567:4567 -v $(pwd)/db:/db wurmlab/sequenceserver