Streamformatics

Repository for the the web-platform developed during my Master of Bioinformatics project at University of Queensland.

This platform consists of two major microbial genomics tools:

Real-time species identification and resistance profiling

Code for this aspect of the platform is named 'analysis' i.e analysis.js or analysis.css.

For information on how to set up and operate this, refer to the wiki entry.

Code for this aspect of the platform is named 'upload' i.e upload.ejs or upload.css.

For further information on the file upload section, refer to the wiki entry.

Code for this aspect of the platform is named 'dashboard' i.e dashboard.js or dashboard.ejs.

For further information on this tool, refer to the wiki entry

You must first have Node.js installed. If you don't already have Node installed you can do so by folllowing the instructions here.

For installing via package managers:

If are you are using Mac and homebrew this is as simple as just running brew install node (you may also ask you to install XCode).
On Linux, check out this page.
For instructions on a Windows, check out this guide.

After you have Node installed, on the command-line, navigate to the directory where you would like to install this repository and run the following:

git clone https://github.com/mbhall88/streamformatics.git
cd streamformatics
npm install

To run the server locally you can either run nodemon or node app.js from the root directory of the repository.

By default this server should be accessible on port 3000. Open a web browser and enter localhost:3000/ into the address bar.