/HiGlass_Galaxy_IE

A HiGlass interactive environment for Galaxy

Primary LanguageMako

HiGlass Galaxy Interactive Environment

This defines the Galaxy interactive environment for HiGlass. It uses the docker container msauria/higlass-ie and is suitable for both local and public instances.

Installation

To install, simply copy this repo into the config/plugins/interactive_environments folder of your Galaxy path.

Configuration

There are two key settings in config/higlass.ini.sample that are required to get this environment running properly.

  1. In order to communicate properly with Galaxy, the docker container needs to know how to connect to the local host running it. This is platform-dependent and currently needs to be manually set. There are three options, one for Linux, Mac, and Windows. Simply uncomment the correct one and make sure the other two are commented out. In addition, make sure that the specified port matches the one that Galaxy is listening to, specified in your config/galaxy.yml file under the parameter 'http'.

  2. For the client-side of Galaxy to be able to communicate with the docker container, it needs to know the ip address and port that the dynamic proxy is using. The port specified in config/galaxy.yml under the parameter 'dynamic_proxy_bind_port'. The ip depends on whether Galaxy is being run as a local or public instance. For a local instance, the ip must match the value of the parameter 'dynamic_proxy_bind_ip' in config/galaxy.yml. A public instance uses the publicly-accessible ip.