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

diff --git src/hg/makeDb/doc/rn6.txt src/hg/makeDb/doc/rn6.txt
index dc58452..2769d06 100644
--- src/hg/makeDb/doc/rn6.txt
+++ src/hg/makeDb/doc/rn6.txt
@@ -4525,15 +4525,36 @@
         -query2Bit=/hive/data/genomes/rn7/rn7.2bit \
         -querySizes=/hive/data/genomes/rn7/chrom.sizes \
         -ooc=/hive/data/genomes/rn6/jkStuff/rn6.11.ooc \
          rn6 rn7
     time (doSameSpeciesLiftOver.pl -verbose=2 \
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
         -query2Bit=/hive/data/genomes/rn7/rn7.2bit \
         -querySizes=/hive/data/genomes/rn7/chrom.sizes \
         -ooc=/hive/data/genomes/rn6/jkStuff/rn6.11.ooc \
          rn6 rn7) > doLiftOverToRn7.log 2>&1
     # real    317m44.103s
 
     # see if the liftOver menus function in the browser from rn6 to rn7
 
 ##############################################################################
+# 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/rn6
+mkdir fantom5
+cd fantom5
+# Making symlinks for big files
+for file in $(ls /hive/data/outside/fantom5/riken_f5/rn6/*.b*) ; do ln -s $file; done
+cd /hive/data/outside/fantom5/riken_f5/rn6/
+cp trackDb.txt fantom5.ra
+vi fantom5.ra
+# Indented subtracks
+# Changing bigDataUrl
+# Removing non-alpha characters
+cd ~/kent/src/hg/makeDb/trackDb/human/rn6
+cp /hive/data/outside/fantom5/riken_f5/rn6/fantom5.ra .
+vi trackDb.ra
+#include fantom5.ra alpha
+##############################################################################