24d667a6353af7e3d009ff35beb21f85dc40984d
hiram
  Tue Dec 20 10:40:08 2022 -0800
correctly make symLinks for chainNet files at the time they actually exist no redmine

diff --git src/hg/utils/automation/doRecipBest.pl src/hg/utils/automation/doRecipBest.pl
index 8ca354c..278d0b8 100755
--- src/hg/utils/automation/doRecipBest.pl
+++ src/hg/utils/automation/doRecipBest.pl
@@ -429,30 +429,42 @@
       $bossScript->add(<<_EOF_
 cd $runDir
 hgLoadChain -test -noBin -tIndex $tDb chainRBest$QDb $tDb.$qDb.rbest.chain.gz
 wget --no-check-certificate -O bigChain.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigChain.as'
 wget --no-check-certificate -O bigLink.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigLink.as'
 sed 's/.000000//' chain.tab | awk 'BEGIN {OFS="\\t"} {print \$2, \$4, \$5, \$11, 1000, \$8, \$3, \$6, \$7, \$9, \$10, \$1}' > chainRBest${QDb}.tab
 bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainRBest${QDb}.tab $targetSizes chainRBest${QDb}.bb
 awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > $QDbLink.tab
 bedToBigBed -type=bed4+1 -as=bigLink.as -tab $QDbLink.tab $targetSizes $QDbLink.bb
 set totalBases = `ave -col=2 $targetSizes | grep "^total" | awk '{printf "%d", \$2}'`
 set basesCovered = `bedSingleCover.pl $QDbLink.tab | ave -col=4 stdin | grep "^total" | awk '{printf "%d", \$2}'`
 set percentCovered = `echo \$basesCovered \$totalBases | awk '{printf "%.3f", 100.0*\$1/\$2}'`
 printf "%d bases of %d (%s%%) in intersection\\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > ../fb.$tDb.chainRBest.$QDb.txt
 rm -f link.tab
 rm -f chain.tab
+if ( -s "\$buildDir/axtChain/chainRBest${QDb}.bb" ) then
+  mkdir -p /gbdb/$tDb/chainNet
+  rm -f "/gbdb/$tDb/chainNet/$tDb.chainRBest$QDb.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest${QDb}Link.bb"
+  ln -s "\$buildDir/axtChain/chainRBest${QDb}.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest$QDb.bb"
+   ln -s "\$buildDir/axtChain/chainRBest${QDb}Link.bb" "/gbdb/$tDb/chainNet/$tDb.chainRBest${QDb}Link.bb"
+endif
+if ( -s "\$buildDir/bigMaf/$tDb.$qDb.rbestNet.bb" ) then
+  mkdir -p /gbdb/$tDb/chainNet
+  rm -f "/gbdb/$tDb/chainNet/$tDb.$qDb.rbestNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.rbestNet.summary.bb"
+  ln -s "\$buildDir/bigMaf/$tDb.$qDb.rbestNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.rbestNet.bb"
+  ln -s "\$buildDir/bigMaf/$tDb.$qDb.rbestNet.summary.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.rbestNet.summary.bb"
+endif
 _EOF_
       );
   }	# else if (! $opt_trackHub && $dbExists)
 
   $bossScript->execute();
 }	#	sub loadRBest {}
 
 sub cleanUp {
   my $runDir = "$buildDir";
   my $whatItDoes = "cleanup temporary files used by RBest procedure.";
   my $bossScript = newBash HgRemoteScript("$runDir/rBestCleanUp.bash", $dbHost,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 rm -fr axtChain/experiments
 rm -f axtChain/bigChain.as axtChain/bigLink.as