3fd174ec070cdd1cd53b276e135c76c869859a4b
gperez2
  Mon Jun 12 00:19:18 2023 -0700
Making FANTOM5 hub into native track, refs #21605

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index cd981b7..353d53e 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35085,16 +35085,37 @@
 # add the rest of the HGNC fields as extra fields except the id and color which are in the first nine
 tawk '{for(ii=5; ii <= 56; ii++) printf("%s\t", $ii); print $ii}' positioned.hg19.txt > tmp2
 paste tmp1 tmp2 | sort -k1,1 -k2,2n > input.bed
 
 # let's do this thing!
 bedToBigBed -extraIndex=name -tab -type=bed9+53 input.bed /cluster/data/hg19/chrom.sizes hgnc.hg19.bb -as=$HOME/kent/src/hg/lib/hgncBig62.as
 
 # put the files into /gbdb
 mkdir -p /gbdb/hg19/hgnc
 rm -rf /gbdb/hg19/hgnc/hgnc.bb
 ln -s `pwd`/hgnc.hg19.bb /gbdb/hg19/hgnc/hgnc.bb 
 
 rm -rf /gbdb/hg19/hgnc/search.ix /gbdb/hg19/hgnc/search.ixx
 ln -s `pwd`/search.hg19.ix /gbdb/hg19/hgnc/search.ix
 ln -s `pwd`/search.hg19.ixx /gbdb/hg19/hgnc/search.ixx
-
+#############################################################################
+# FANTOM5 refs #21605 (2023-06-09 Gerardo)
+cd /hive/data/outside/
+mkdir fantom5
+cd fantom5
+hubClone -download https://fantom.gsc.riken.jp/5/datahub/hub.txt
+cd /gbdb/hg19
+mkdir fantom5
+cd fantom5
+# Making symlinks for big files
+for file in $(ls /hive/data/outside/fantom5/riken_f5/hg19/*.b*) ; do ln -s $file; done
+cd /hive/data/outside/fantom5/riken_f5/hg19/
+cp trackDb.txt fantom5.ra
+vi fantom5.ra
+# Indented subtracks
+# Changing bigDataUrl
+# Removing non-alpha characters
+cd ~/kent/src/hg/makeDb/trackDb/human/hg19
+cp /hive/data/outside/fantom5/riken_f5/hg19/fantom5.ra .
+vi trackDb.ra
+#include fantom5.ra alpha
+#############################################################################