c72e86438227987b38863408b636fa101a4cea39
hiram
  Mon Mar 4 16:48:30 2024 -0800
liftOver to panTro5 per user request refs #33047

diff --git src/hg/makeDb/doc/panTro2.txt src/hg/makeDb/doc/panTro2.txt
index 5156135..21a07e0 100644
--- src/hg/makeDb/doc/panTro2.txt
+++ src/hg/makeDb/doc/panTro2.txt
@@ -3396,16 +3396,41 @@
     hgsql panTro2 -e "INSERT INTO grp VALUES ('denisova', 'Denisova Assembly and Analysis', 6.6);"
 
 ############################################################################
 # construct liftOver to panTro3 (DONE - 2011-02-22 - Hiram) 
     cd /hive/data/genomes/panTro2/bed
     mkdir blat.panTro3.2011-02-22
     cd blat.panTro3.2011-02-22
     time doSameSpeciesLiftOver.pl -buildDir=`pwd` -bigClusterHub=swarm \
 	-dbHost=hgwdev -workhorse=hgwdev panTro2 panTro3 > do.log 2>&1
     #	real    84m22.796s
 
     # check /gbdb/panTro2/liftOver for new file there to panTro3
     # verify convert functions on genome-test panTro2 to panTro3
     # and file is present on htdocs-hgdownload/goldenPath/panTro2/liftOver
 
-############################################################################
+##############################################################################
+# construct liftOver to panTro5 (DONE - 2024-02-26 - Hiram) 
+    ssh hgwdev
+    mkdir /hive/data/genomes/panTro2/bed/blat.panTro5.2024-02-26
+    cd /hive/data/genomes/panTro2/bed/blat.panTro5.2024-02-26
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/panTro2/panTro2.2bit \
+        -targetSizes=/hive/data/genomes/panTro2/chrom.sizes \
+        -query2Bit=/hive/data/genomes/panTro5/panTro5.2bit \
+        -querySizes=/hive/data/genomes/panTro5/chrom.sizes \
+        -ooc=/hive/data/genomes/panTro2/11.ooc \
+         panTro2 panTro5
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/panTro2/panTro2.2bit \
+        -targetSizes=/hive/data/genomes/panTro2/chrom.sizes \
+        -query2Bit=/hive/data/genomes/panTro5/panTro5.2bit \
+        -querySizes=/hive/data/genomes/panTro5/chrom.sizes \
+        -ooc=/hive/data/genomes/panTro2/11.ooc \
+         panTro2 panTro5) > doLiftOverToPanTro5.log 2>&1
+    # real    1599m46.101s
+
+    # see if the liftOver menus function in the browser from panTro2 to panTro5
+
+##############################################################################