quickTrackHub

quickTrackHub.pl generates a UCSC Genome Track Hub based on a list of UCSC-compatible genome data files and a JSON Track Hub Definition File (THDF). The list of data files to include must be specified in a text file, one data file path per line. The path to this list is specified in the dataFilesList JSON property of the THDF. An example of a THDF is included in this repository (trackHubDefinition.json).

Usage

Copy trackHubDefinition.json to your target, web-accessible directory, and edit it according to your needs. The values of the following properties must be changed:

• trackHubAssociatedEmail: your email

• webPublicDir: the HTTP/FTP address of your data directory where the Hub will be output

• dataFilesList: the local path to the list of data files (one per line) to include in the hub

Then run the following command from within your target directory, in which the Track Hub will be created:

quickTrackHub.pl trackHubDefinition.json

(This command will work only if quickTrackHub.pl lies in a directory which is included in your $PATH)

Perl module dependencies:

Standard CPAN modules

File::Basename
JSON
FindBin

Custom module

(included in this repository, must be in same directory as quickTrackHub.pl in your local installation):

processJsonToHash