Track Hub Example

Venkat, of ENCODE3 at Stanford, has a trackhubtest repository you can check out from github to add to your public_html folder to create your own example Track Hub. By copying the example, it provides a means to explore the mechanics of Hubs by adding lines and editing the Hub.

Web address of Venkat's GitHub repository:

• https://github.com/vsmalladi?tab=repositories

From your command line in a directory in your public_html directory use the following command to clone the repository:

• git clone git://github.com/vsmalladi/trackhubtest.git

Then create a link to the hub.txt file, for example if hub.txt is in the directory where you cloned it, such as, /cluster/home/brianlee/public_html/trackHubTestVenkat/VenkatClone/trackhubtest/, you can create a URL to access the hub.txt file from your directory (example):

• http://hgwdev.gi.ucsc.edu/~brianlee/trackHubTestVenkat/VenkatClone/trackhubtest/hub.txt BROKEN

Drop your URL in the "My Hubs" page and change visibility to see the different tracks:

• http://hgwbeta.cse.ucsc.edu/cgi-bin/hgHubConnect?

By making copies and changes to the Hub architecture, you can explore Hub architecture. An excellent easy "Homework Problem" is to take all the individual .txt files in the hg19/ directory and put them in the trackDb.txt file where they would normally live (replacing every "include xxx.txt" line with the text that is broken out in an external file).