# Eukaryotic Promoter Database (EPD)
#       at Swiss Bioinformatic Institute
# Contact:  Phillipe Bucher

# Tracks for human (hg19, hg38) and mouse (mm10)
# Coding and non-coding subtracks (except for hg19, just coding)

# Note: there is a public hub including supporting annotations and many more genomes

#(2019-11-05 kate)

##########################################################
# Get lastest human annotations

# version 006, 6/16/18

mkdir human006
cd human006
wget ftp://ccg.epfl.ch/epdnew/H_sapiens/006/\*
mkdir db
cd db
wget ftp://ccg.epfl.ch/epdnew/H_sapiens/006/db/\*
cd ..
ln -s `pwd`/Hs_EPDnew_006_hg19.bb /gbdb/hg19/bbi/epdNewHuman006.hg19.bb
ln -s `pwd`/Hs_EPDnew_006_hg38.bb /gbdb/hg38/bbi/epdNewHuman006.hg38.bb

# and non-coding
cd ..
mkdir humanNc001
cd humanNc001
wget ftp://ccg.epfl.ch/epdnew/human_nc/001/\*
cd ..
ln -s `pwd`/HsNC_EPDnew_001_hg38.bb /gbdb/hg38/bbi/epdNewHumanNc001.hg38.bb

##########################################################
# Get latest mouse annotations

# 003

mkdir mouse003
cd mouse003
wget ftp://ccg.epfl.ch/epdnew/M_musculus/003/\*
ln -s `pwd`/Mm_EPDnew_003_mm10.bb /gbdb/mm10/bbi/epdNewMouse003.mm10.bb

cd ..
mkdir mouseNc001
cd mouseNc001
wget ftp://ccg.epfl.ch/epdnew/mouse_nc/001/\*
ln -s `pwd`/MmNC_EPDnew_001_mm10.bb /gbdb/mm10/bbi/epdNewMouseNc001.mm10.bb