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

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 5a74738..7246231 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18750,15 +18750,36 @@
         -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
  -target2Bit=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.2bit \
  -targetSizes=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.chrom.sizes \
         -query2Bit=/hive/data/genomes/mm10/mm10.2bit \
         -querySizes=/hive/data/genomes/mm10/chrom.sizes \
         -ooc=/hive/data/genomes/asmHubs/genbankBuild/GCA/001/624/675/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.11.ooc \
          GCA_001624675.1 mm10) > doLiftOverToMm10.log 2>&1
 XXX running Fri Jan 20 14:46:36 PST 2023
 
     # real    244m28.766s
 
     # see if the liftOver menus function in the browser from mm10
     #    to GCA_001624675.1
 
 ##############################################################################
+# 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/mm10
+mkdir fantom5
+cd fantom5
+# Making symlinks for big files
+for file in $(ls /hive/data/outside/fantom5/riken_f5/mm10/*.b*) ; do ln -s $file; done
+cd /hive/data/outside/fantom5/riken_f5/mm10/
+cp trackDb.txt fantom5.ra
+vi fantom5.ra
+# Indented subtracks
+# Changing bigDataUrl
+# Removing non-alpha characters
+cd ~/kent/src/hg/makeDb/trackDb/mouse/mm10/
+cp /hive/data/outside/fantom5/riken_f5/hg38/fantom5.ra .
+vi trackDb.ra
+#include fantom5.ra alpha
+##############################################################################