QUASI-Express

Getting Started

These instructions will get you a copy of the project up and running on your local machine for your own purposes.

Prerequisites

• NodeJS
• MongoDB

Ubuntu Linux

First, make sure you have the neccessary tools for building software from GitHub installed (needed for compilation/building/etc). If not install them like this

sudo apt-get install -y build-essential git curl

Next, install NodeJS itself and confirm the version you downloaded (e.g. v9.6.1)

curl -sL https://deb.nodesource.com/setup_9.x | sudo -E bash -
sudo apt-get install -y nodejs
node --version

MongoDB is needed as the backend part. You can find a detailed installation instruction here: Link

Installing

Download the repository to your local machine and change to the new folder. Once inside the new folder, trigger the installation of all required npm dependencies

git clone https://github.com/markonyango/quasi-express.git
cd quasi-express
npm install

Next install the quasi-tools library for full functionality. It's available here: Link

git clone https://github.com/markonyango/quasi-tools.git
sh ./quasi-tools/install.sh

The server can be started by simply running either of the following commands

npm start
./bin/www

the difference being that the first starts the server with nodemon which will catch app crashes and restart the server, while the latter starts the server instance directly.

With the default setup, the server will be reachable localhost:3000. Every other PC in your network will also be able to access the server as long as your PCs network/firewall settings allow it. This is usefull if you are thinking of setting up the server to be used by multiple people (e.g. co-workers in your group or even faculty/company-wide).

Configuring the server

Once the server was successfully downloaded, make sure to set the neccessary server variables in settings.js:

module.exports = {
  uploadPath: 'path/where/userfiles/will/be/stored',
  mongodDB: 'url to your mongodb installation (e.g. 127.0.0.1)',
  alignReferenceFolder: 'path/to/your/bowtie/reference/files'
}

Running the tests

To run the testsuite, spin up the server with

npm start

and visit localhost:3000/test in your browser. Each test will run automatically and report its return status. The server will also provide useful information in the terminal window from which it was started. Detailed information pertaining potential errors during execution will show up there.

Make sure that you remove the following files once you are ready to publicly deploy the server (for obvious security reasons)

• public/test (entire folder)
• public/js/test.js
• public/js/mocha.min.js
• public/js/chai.min.js
• views/test.hbs

These files are only used for testing purposes and can be remove safely after successful testing your installation.

Authors

• Mark Onyango - Initial work - markonyango

License

This project is licensed under the GPLv3 License - see the LICENSE.md file for details

Acknowledgments

• Hat tip to anyone whose code was used