66b1030888d2fbc504ed737350256b20442367c7
braney
  Fri Sep 3 10:43:22 2021 -0700
ongoing work on knownGene automation

diff --git src/hg/utils/otto/knownGene/buildBlast.sh src/hg/utils/otto/knownGene/buildBlast.sh
index e3dafda..f72f856 100755
--- src/hg/utils/otto/knownGene/buildBlast.sh
+++ src/hg/utils/otto/knownGene/buildBlast.sh
@@ -34,31 +34,30 @@
 ${yeastDb}Fa $yeastFa
 
 buildDir $dir/hgNearBlastp
 scratchDir $scratchDir/brHgNearBlastp
 ThisEnd
 ) > config.ra
 
 rm -rf  $scratchDir/brHgNearBlastp
 doHgNearBlastp.pl -noLoad -clusterHub=ku -distrHost=hgwdev -dbHost=hgwdev -workhorse=hgwdev config.ra 
 
 # Load self
 cd $dir/hgNearBlastp/run.$tempDb.$tempDb
 # builds knownBlastTab
 ./loadPairwise.csh
 
-# Load human and rat
 cd $dir/hgNearBlastp/run.$tempDb.$xdb
 hgLoadBlastTab $tempDb $xBlastTab -maxPer=1 out/*.tab
 cd $dir/hgNearBlastp/run.$tempDb.$ratDb
 hgLoadBlastTab $tempDb $rnBlastTab -maxPer=1 out/*.tab
 
 # Remove non-syntenic hits for human and rat
 # Takes a few minutes
 mkdir -p /gbdb/$tempDb/liftOver
 rm -f /gbdb/$tempDb/liftOver/${tempDb}To$RatDb.over.chain.gz /gbdb/$tempDb/liftOver/${tempDb}To$Xdb.over.chain.gz
 ln -s $genomes/$db/bed/liftOver/${db}To$RatDb.over.chain.gz \
     /gbdb/$tempDb/liftOver/${tempDb}To$RatDb.over.chain.gz
 ln -s $genomes/$db/bed/liftOver/${db}To${Xdb}.over.chain.gz \
     /gbdb/$tempDb/liftOver/${tempDb}To$Xdb.over.chain.gz
 
 # delete non-syntenic genes from rat and mouse blastp tables