#Lou 5/24/2022

mkdir /hive/data/genomes/hg38/bed/genCC
cd /hive/data/genomes/hg38/bed/genCC

wget https://search.thegencc.org/download/action/submissions-export-tsv

#At this stage I had to do some manual curation of the file. Mostly there were a bunch
#of newlines in the 'info' column of the file which were being parsed as new entries.
#Also there were some extra tab characters present in a few of the fields. In total
#fewer than 20 changes were made directly to the file

#Both hg19 and hg38 tracks were created by creating a bed file out of the hg38 MANE1.0 bigBed
#and running the following python3 script

kent/src/hg/makeDb/scripts/genCC/doGenCC.py

#Lastly symbolic links were made
ln -s /hive/data/genomes/hg38/bed/genCC/hg38genCC.bb /gbdb/hg38/bbi/genCC.bb
ln -s /hive/data/genomes/hg38/bed/genCC/hg19genCC.bb /gbdb/hg19/bbi/genCC.bb