Web-based visualization of large, high-dimensional datasets.
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README.md

Faerun

If you use this code or application, please cite the original paper published by Bioinformatics: 10.1093/bioinformatics/btx760

Faerun

Visualizing large high-dimensional datasets.

For a complete overview and detailed installation instructions for this project, please visit the project website.

Faerun

This is the front-end of the FUn framework. A reference implementation visualizing over 10 million compunds exported from the SureChEMBL database can be found at faerun.gdb.tools. The backend can be found in its own github repository.

Getting Started

The best way to get started with Faerun is to pull the respective Docker Image.

docker run -d -p 80:80 --name faerun daenuprobst/faerun

This will use the default configuration. Using the default configuration means, that faerun will connect to the default services provided by our research group (http://www.gdb.unibe.ch). If you wish to provide your own service (e.g. containing other databases) you can provide a custom server address using the environment variable SERVER

docker run -d -p 80:80 -e SERVER=ws://example.ch/underdark --name faerun daenuprobst/faerun

See how to deploy your own backend server here.

If you wish to change more than just the server providing the data sets, you will either have to clone this repository and build the app and then create your own docker image or you can run docker using the following command and edit the configuration file on the host

docker run -d -p 80:80 -v /your/host/dir:/usr/share/nginx/html --name faerun daenuprobst/faerun

All application files will then be stored in the directory /your/host/dir on your host and you are able to make changes to the configuration file config.js.

Building Faerun

Dependencies:

  • nodejs, npm
  • gulp (install using npm install -g gulp)

In order to (hack and) build faerun, first clone this repository git clone https://github.com/reymond-group/faerun.git and then run npm install in the folder where you cloned faerun into (default: faerun). To build faerun run gulp, which will create the distribution folder dist, the contents of which you can copy and serve on any web server such as nginx, IIS or apache.

Common Problems

  • If you are cannot get the container running after building it yourself on a Windows machine, you might have hidden windows characters in the entrypoint.sh script. Please remove them using dos2unix.exe (http://waterlan.home.xs4all.nl/dos2unix.html) and try to run the container again.