97cc4f47f34fca7bebb8bc8733d54a57a8d98839
hiram
  Fri Dec 9 14:25:51 2022 -0800
liftOver canFam6 to canFam2 refs #30374

diff --git src/hg/makeDb/doc/canFam6/initialBuild.txt src/hg/makeDb/doc/canFam6/initialBuild.txt
index 2a3b381..1b54cd9 100644
--- src/hg/makeDb/doc/canFam6/initialBuild.txt
+++ src/hg/makeDb/doc/canFam6/initialBuild.txt
@@ -1299,16 +1299,41 @@
     # 63 redmine.canFam6.table.list
 
     # how many actual:
     awk -F'.' '{printf "hgsql -N %s -e '"'"'show table status like \"%s\";'"'"'\n", $1, $2}' redmine.canFam6.table.list | sh | wc -l
     # 63
 
     # would be a smaller number actual if some were missing
 
     # add the path names to the listing files in the redmine issue
     # in the three appropriate entry boxes:
 
 #	/hive/data/genomes/canFam6/pushQ/redmine.canFam6.file.list
 #	/hive/data/genomes/canFam6/pushQ/redmine.canFam6.releaseLog.txt
 #	/hive/data/genomes/canFam6/pushQ/redmine.canFam6.table.list
 
-#########################################################################
+##############################################################################
+# LIFTOVER TO canFam2 (DONE - 2022-12-07 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/canFam6/bed/blat.canFam2.2022-12-07
+    cd /hive/data/genomes/canFam6/bed/blat.canFam2.2022-12-07
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -targetSizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -querySizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
+         canFam6 canFam2
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/canFam6/canFam6.2bit \
+        -targetSizes=/hive/data/genomes/canFam6/chrom.sizes \
+        -query2Bit=/hive/data/genomes/canFam2/canFam2.2bit \
+        -querySizes=/hive/data/genomes/canFam2/chrom.sizes \
+        -ooc=/hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc \
+         canFam6 canFam2) > doLiftOverToCanFam2.log 2>&1
+    # real    2179m29.114s
+
+    # see if the liftOver menus function in the browser from canFam6 to canFam2
+
+##############################################################################