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)
and CSS files.
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