586d901c9bb52863a5518271533f7ff87972843b
hiram
  Tue Jul 4 12:12:00 2023 -0700
correctly setup the synNet gbdb links no redmine

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index b8bdaca..b42db8a 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1831,36 +1831,30 @@
   awk 'BEGIN {OFS="\\t"} {print \$1, \$2, \$3, \$5, \$4}' link.tab | sort -k1,1 -k2,2n > chainSyn${QDb}Link.tab
   bedToBigBed -type=bed4+1 -as=bigLink.as -tab chainSyn${QDb}Link.tab $defVars{SEQ1_LEN} chainSyn${QDb}Link.bb
   set totalBases = `ave -col=2 $defVars{SEQ1_LEN} | grep "^total" | awk '{printf "%d", \$2}'`
   set basesCovered = `bedSingleCover.pl chainSyn${QDb}Link.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.$tDb.chainSyn${QDb}Link.txt
 netFilter -minGap=10 $tDb.$qDb.syn.net.gz \\
   | hgLoadNet -test -noBin -warn -verbose=0 $tDb netSyn$QDb stdin
 mv align.tab netSyn$QDb.tab
 if ( -s "$buildDir/axtChain/chainSyn${QDb}.bb" ) then
   mkdir -p /gbdb/$tDb/chainNet
   rm -f "/gbdb/$tDb/chainNet/$tDb.chainSyn$QDb.bb" "/gbdb/$tDb/chainNet/$tDb.chainSyn${QDb}Link.bb"
   ln -s "$buildDir/axtChain/chainSyn${QDb}.bb" "/gbdb/$tDb/chainNet/$tDb.chainSyn$QDb.bb"
   ln -s "$buildDir/axtChain/chainSyn${QDb}Link.bb" "/gbdb/$tDb/chainNet/$tDb.chainSyn${QDb}Link.bb"
 endif
-if ( -s "$buildDir/bigMaf/$tDb.$qDb.synNet.bb" ) then
-  mkdir -p /gbdb/$tDb/chainNet
-  rm -f "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.summary.bb"
-  ln -s "$buildDir/bigMaf/$tDb.$qDb.synNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.bb"
-  ln -s "$buildDir/bigMaf/$tDb.$qDb.synNet.summary.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.summary.bb"
-endif
 endif
 rm -f link.tab
 rm -f chain.tab
 _EOF_
       );
     }
 
     $bossScript->add(<<_EOF_
 if (\$lineCount > 0) then
   netToAxt $tDb.$qDb.syn.net.gz $tDb.$qDb.all.chain.gz \\
     $defVars{'SEQ1_DIR'} $defVars{'SEQ2_DIR'} stdout \\
     | axtSort stdin stdout \\
     | axtToMaf -tPrefix=$tDb. -qPrefix=$qDb. stdin \\
       $defVars{SEQ1_LEN} $defVars{SEQ2_LEN} \\
       stdout \\
@@ -1877,30 +1871,36 @@
   wget --no-check-certificate -O bigMaf.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/bigMaf.as'
   wget --no-check-certificate -O mafSummary.as 'http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/mafSummary.as'
   mafToBigMaf $tDb ../axtChain/$tDb.$qDb.synNet.maf.gz stdout \\
     | sort -k1,1 -k2,2n > $tDb.$qDb.synNet.txt
   bedToBigBed -itemsPerSlot=4 -type=bed3+1 -as=bigMaf.as -tab  $tDb.$qDb.synNet.txt \\
     $defVars{SEQ1_LEN} $tDb.$qDb.synNet.bb
   hgLoadMafSummary -minSeqSize=1 -test $tDb $tDb.$qDb.synNet.summary \\
         ../axtChain/$tDb.$qDb.synNet.maf.gz
   cut -f2- $tDb.$qDb.synNet.summary.tab | sort -k1,1 -k2,2n \\
         > $tDb.$qDb.synNet.summary.bed
   bedToBigBed -type=bed3+4 -as=mafSummary.as -tab \\
         $tDb.$qDb.synNet.summary.bed \\
         $defVars{SEQ1_LEN} $tDb.$qDb.synNet.summary.bb
   rm -f $tDb.$qDb.synNet.txt $tDb.$qDb.synNet.summary.tab \\
         $tDb.$qDb.synNet.summary.bed
+  if ( -s "$buildDir/bigMaf/$tDb.$qDb.synNet.bb" ) then
+    mkdir -p /gbdb/$tDb/chainNet
+    rm -f "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.summary.bb"
+    ln -s "$buildDir/bigMaf/$tDb.$qDb.synNet.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.bb"
+    ln -s "$buildDir/bigMaf/$tDb.$qDb.synNet.summary.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.synNet.summary.bb"
+  endif
 endif
 _EOF_
       );
     }
 
     if (! $opt_skipDownload) {
       $bossScript->add(<<_EOF_
 mkdir -p $goldenPath/$tDb/vs$QDb
 cd $goldenPath/$tDb/vs$QDb
 if (-s $runDir/synNet.md5sum.txt ) then
   rm -f $tDb.$qDb.syn.net.gz
   rm -f $tDb.$qDb.synNet.maf.gz
   ln -s $runDir/$tDb.$qDb.syn.net.gz .
   ln -s $runDir/$tDb.$qDb.synNet.maf.gz .
   cat $runDir/synNet.md5sum.txt >> md5sum.txt