960327879cd684b279610a26bcd311625c401b02
hiram
  Tue Jan 31 11:17:32 2023 -0800
incorrect buildDir variable in the netSyntenic step fixed no redmine

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 9c89d2a..b8bdaca 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1825,41 +1825,41 @@
 if (\$lineCount > 0) then
   hgLoadChain -test -noBin -tIndex $tDb chainSyn$QDb $tDb.$qDb.syn.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}' > chainSyn${QDb}.tab
   bedToBigBed -type=bed6+6 -as=bigChain.as -tab chainSyn${QDb}.tab $defVars{SEQ1_LEN} chainSyn${QDb}.bb
   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
+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${QDb}Link.bb"
+  ln -s "$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.$qDb.synNet.bb" ) then
+if ( -s "$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.$qDb.synNet.summary.bb"
+  ln -s "$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} \\