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

diff --git src/hg/makeDb/doc/canFam3.txt src/hg/makeDb/doc/canFam3.txt
index 6bc195b..0465f34 100644
--- src/hg/makeDb/doc/canFam3.txt
+++ src/hg/makeDb/doc/canFam3.txt
@@ -2039,15 +2039,36 @@
 # intron_variant,
 # non_coding_transcript_exon_variant,
 # upstream_gene_variant,
 # downstream_gene_variant,
 # intergenic_variant,
 # no_sequence_alteration,
 
 # add new filter lines to trackDb
 # filterValues.varClass (new name for same field -- orig EVA class
 # filterValues.ucscClass missense_variant,frameshift_variant,inframe_deletion,inframe_insertion,initiator_codon_variant,stop_gained,stop_lost,splice_acceptor_variant,splice_donor_variant,splice_region_variant,exon_loss_variant,coding_sequence_variant,5_prime_UTR_variant,3_prime_UTR_variant,NMD_transcript_variant,synonymous_variant,stop_retained_variant,complex_transcript_variant,non_coding_transcript_exon_variant,intron_variant,upstream_gene_variant,downstream_gene_variant,intergenic_variant,no_sequence_alteration,  
 
 # drop old filter lines (no longer using RS_VALIDATED field
 filterValues.valid No,Yes
 
 ##############################################################################
+# 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/canFam3
+mkdir fantom5
+cd fantom5
+# Making symlinks for big files
+for file in $(ls /hive/data/outside/fantom5/riken_f5/canFam3/*.b*) ; do ln -s $file; done
+cd /hive/data/outside/fantom5/riken_f5/canFam3/
+cp trackDb.txt fantom5.ra
+vi fantom5.ra
+# Indented subtracks
+# Changing bigDataUrl
+# Removing non-alpha characters
+cd ~/kent/src/hg/makeDb/trackDb/human/canFam3
+cp /hive/data/outside/fantom5/riken_f5/canFam3/fantom5.ra .
+vi trackDb.ra
+#include fantom5.ra alpha
+##############################################################################