7b0c8bb2cb0e36f4b8a3335dfe755586cbdf584f
hiram
  Wed Dec 7 21:32:28 2022 -0800
liftOver per user request 4 to 9 to 4 refs #30301

diff --git src/hg/makeDb/doc/bosTau9/initialBuild.txt src/hg/makeDb/doc/bosTau9/initialBuild.txt
index 7b61206..70c5978 100644
--- src/hg/makeDb/doc/bosTau9/initialBuild.txt
+++ src/hg/makeDb/doc/bosTau9/initialBuild.txt
@@ -1160,16 +1160,41 @@
     sed -i -e "/Tandem Dups/d" redmine.bosTau9.releaseLog.txt
     sed -i -e "/gapOverlap/d" redmine.bosTau9.table.list
     sed -i -e "/Gap Overlaps/d" redmine.bosTau9.releaseLog.txt
 
     #   check for errors in stderr.out, some are OK, e.g.:
     # WARNING: bosTau9 does not have seq
     # WARNING: bosTau9 does not have extFile
 
     # add the path names to the listing files in the redmine issue
     # in the three appropriate entry boxes:
 
 /hive/data/genomes/bosTau9/pushQ/redmine.bosTau9.file.list
 /hive/data/genomes/bosTau9/pushQ/redmine.bosTau9.releaseLog.txt
 /hive/data/genomes/bosTau9/pushQ/redmine.bosTau9.table.list
 
-#########################################################################
+##############################################################################
+# LIFTOVER TO bosTau4 (DONE - 2022-12-06 - Hiram)
+    ssh hgwdev
+    mkdir /hive/data/genomes/bosTau9/bed/blat.bosTau4.2022-12-06
+    cd /hive/data/genomes/bosTau9/bed/blat.bosTau4.2022-12-06
+    doSameSpeciesLiftOver.pl -verbose=2 \
+        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/bosTau9/bosTau9.2bit \
+        -targetSizes=/hive/data/genomes/bosTau9/chrom.sizes \
+        -query2Bit=/hive/data/genomes/bosTau4/bosTau4.2bit \
+        -querySizes=/hive/data/genomes/bosTau4/chrom.sizes \
+        -ooc=/hive/data/genomes/bosTau9/jkStuff/bosTau9.11.ooc \
+         bosTau9 bosTau4
+    time (doSameSpeciesLiftOver.pl -verbose=2 \
+        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
+        -target2Bit=/hive/data/genomes/bosTau9/bosTau9.2bit \
+        -targetSizes=/hive/data/genomes/bosTau9/chrom.sizes \
+        -query2Bit=/hive/data/genomes/bosTau4/bosTau4.2bit \
+        -querySizes=/hive/data/genomes/bosTau4/chrom.sizes \
+        -ooc=/hive/data/genomes/bosTau9/jkStuff/bosTau9.11.ooc \
+         bosTau9 bosTau4) > doLiftOverToBosTau9.log 2>&1
+    # real    384m15.787s
+
+    # see if the liftOver menus function in the browser from bosTau9 to bosTau4
+
+##############################################################################