76fba02a1a3d0f8a66beebaafce75b2770407522
hiram
  Tue Jun 16 12:54:12 2020 -0700
liftOvers to panPan3 refs #25720

diff --git src/hg/makeDb/doc/panPan2/initialBuild.txt src/hg/makeDb/doc/panPan2/initialBuild.txt
index 5b1620a..efa3b62 100644
--- src/hg/makeDb/doc/panPan2/initialBuild.txt
+++ src/hg/makeDb/doc/panPan2/initialBuild.txt
@@ -683,16 +683,35 @@
 
     #   check for errors in stderr.out, some are OK, e.g.:
     # WARNING: hgwdev does not have /gbdb/panPan2/wib/gc5Base.wib
     # WARNING: hgwdev does not have /gbdb/panPan2/wib/quality.wib
     # WARNING: hgwdev does not have /gbdb/panPan2/bbi/quality.bw
     # WARNING: panPan2 does not have seq
     # WARNING: panPan2 does not have extFile
 
     #   copy it to hgwbeta
     #   copy it to hgwbeta
     scp -p panPan2.pushQ.sql qateam@hgwbeta:/tmp/
     ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/panPan2.pushQ.sql"
     #   in that pushQ entry walk through each entry and see if the
     #   sizes will set properly
 
+##############################################################################
+# LIFTOVER TO panPan3 (DONE - 2020-06-15 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/panPan2/bed/blat.panPan3.2020-06-15
+    cd /hive/data/genomes/panPan2/bed/blat.panPan3.2020-06-15
+
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -ooc=/hive/data/genomes/panPan2/jkStuff/panPan2.11.ooc \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+         panPan2 panPan3
+
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -ooc=/hive/data/genomes/panPan2/jkStuff/panPan2.11.ooc \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+         panPan2 panPan3) > doLiftOverToPanPan3.log 2>&1
+    # real    312m42.976s
+
+    # verify this functions in the genome browser from panPan2 to panPan3
+
 #########################################################################