Intuitive local web frontend for the BLAST bioinformatics tool
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Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Latest commit 3e04d4e Jan 15, 2019
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README.md

build status code climate coverage gem version total downloads

gitter chat

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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 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.

Install and configure

To install the old, stable version - 1.0.11 - please see http://sequenceserver.com.

To get the latest 1.1.0-beta release, run:

gem install --pre sequenceserver

Version 1.1.0-beta releases are announced on Google Group. Summary of changes can also be viewed on our GitHub release page.

Develop and contribute

You will need Ruby and RubyGems, Node and npm, and CodeClimate.

Setup

Get source code and install dependencies.

git clone https://github.com/wurmlab/sequenceserver
gem install bundler
cd sequenceserver
npm install
bundle

If you just want to install and use SequenceServer from source you can skip npm install step, and skip installing gems used for testing:

git clone https://github.com/wurmlab/sequenceserver
gem install bundler
cd sequenceserver
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 tests:

bundle exec rspec

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

codeclimate analyze

Build minifies JS and CSS bundles:

npm run-script build

Using Docker

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

Contact

Big Thanks

Cross-browser Testing Platform and Open Source <3 Provided by Sauce Labs