Pipeline that creates Ensembl plant track hubs given ENA study ids and puts them in the Ensembl Track Hub Registry.
The track hubs contain the Array Express' alignments of Ensembl plant genomes to the RNAseq data available in ENA.
Array Express provides the .cram files of the alignments and using their REST API the pipeline communicates with the AE data.
Every track hub represents an ENA study. A track hub can have more than 1 plant species. The tracks of the track hubs are the CRAM alignement files.
Pipeline:
pipeline_create_register_track_hubs.pl
Parameters:
-server_dir_full_path (location of where the track hub files to be stored)
-server_url (server url of the location of the track hubs)
-th_visibility (values accepted: public/hidden -> whether the TH registered in the THR will be public or not)
-do_track_hubs_from_scratch (optional flag)
Example run:
perl pipeline_create_register_track_hubs.pl -server_dir_full_path full_path_for_storing_the_ths -server_url url_of_the_directory_of_the_ths -th_visibility public -do_track_hubs_from_scratch 1> output 2>std_errors