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 Experess' 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:
-THR_username etapanari (of the track Hub Registry account)
-THR_password (of the track Hub Registry account)
-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)
-do_track_hubs_from_scratch (optional flag)
Example run:
perl pipeline_create_register_track_hubs.pl -THR_username etapanari -THR_password testing -server_dir_full_path /nfs/ensemblgenomes/ftp/pub/misc_data/.TrackHubs/ena_warehouse_meta/testing -server_url ftp://ftp.ensemblgenomes.org/pub/misc_data/.TrackHubs/ena_warehouse_meta/testing -do_track_hubs_from_scratch 1> output 2>std_errors