e83574e4d897147878ee3f50d7c37e49e30effa8
hiram
  Fri Aug 9 09:16:55 2024 -0700
eliminate the /gbdb/GC* symlinks for bigBed files no redmine

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 7e36792..d7ee13b 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1206,31 +1206,31 @@
 
 cd \$buildDir
 featureBits $tDb $QDbLink >&fb.$tDb.$QDbLink.txt
 cat fb.$tDb.$QDbLink.txt
 _EOF_
       );
     } else {	# not a database assembly
       $bossScript->add(<<_EOF_
 cp -p noClass.net $tDb.$qDb.net
 netFilter -minGap=10 noClass.net \\
   | hgLoadNet -test -noBin -warn -verbose=0 $tDb net$QDb stdin
 mv align.tab net$QDb.tab
 _EOF_
       );
       # target may be database assembly, special set of gbdb symLinks
-      if ($dbExists && $tChromInfoExists) {
+      if ( $dbExists && $tChromInfoExists && $tDb !~ m/^GC/ ) {
       $bossScript->add(<<_EOF_
 if ( -s "\$buildDir/axtChain/chain${QDb}.bb" ) then
   mkdir -p /gbdb/$tDb/chainNet
   rm -f "/gbdb/$tDb/chainNet/$tDb.chain$QDb.bb" "/gbdb/$tDb/chainNet/$tDb.chain${QDb}Link.bb"
   ln -s "\$buildDir/axtChain/chain${QDb}.bb" "/gbdb/$tDb/chainNet/$tDb.chain$QDb.bb"
   ln -s "\$buildDir/axtChain/chain${QDb}Link.bb" "/gbdb/$tDb/chainNet/$tDb.chain${QDb}Link.bb"
 endif
 if ( -s "\$buildDir/bigMaf/$tDb.$qDb.net.bb" ) then
   mkdir -p /gbdb/$tDb/chainNet
   rm -f "/gbdb/$tDb/chainNet/$tDb.$qDb.net.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.net.summary.bb"
   ln -s "\$buildDir/bigMaf/$tDb.$qDb.net.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.net.bb"
   ln -s "\$buildDir/bigMaf/$tDb.$qDb.net.summary.bb" "/gbdb/$tDb/chainNet/$tDb.$qDb.net.summary.bb"
 endif
 _EOF_
       );
@@ -1603,31 +1603,30 @@
   }
   if (! -e $successFile && ! $opt_debug) {
     die "installDownloads: looks like previous stage was not successful " .
       "(can't find $successFile).\n";
   }
   my $goldenPath = $HgAutomate::goldenPath;
   if ($tDb =~ m/^GC/) {
      $goldenPath = &HgAutomate::asmHubDownloadDir($tDb);
   }
   &dumpDownloadReadme("$runDir/README.txt");
   my $over = $tDb . "To$QDb.over.chain.gz";
   my $liftOverDir = "$HgAutomate::clusterData/$tDb/$HgAutomate::trackBuild/liftOver";
   if ($tDb =~ m/^GC/) {
      $liftOverDir = &HgAutomate::asmHubBuildDir($tAsmId) . "/liftOver";
   }
-printf STDERR "# DBG: tDb '%s' have liftOverDir: '%s'\n", $tDb, $liftOverDir;
   my $gpLiftOverDir = "$goldenPath/$tDb/liftOver";
   my $gbdbLiftOverDir = "$HgAutomate::gbdb/$tDb/liftOver";
   my $andNets = $isSelf ? "." :
     ", nets and axtNet,\n" .
     "# and copies the liftOver chains to the liftOver download dir.";
   my $whatItDoes = "It creates the download directory for chains$andNets";
   my $bossScript = new HgRemoteScript("$runDir/installDownloads.csh", $dbHost,
 				      $runDir, $whatItDoes, $DEF);
   $bossScript->add(<<_EOF_
 mkdir -p $goldenPath/$tDb
 rm -rf $goldenPath/$tDb/vs$QDb
 mkdir -p $goldenPath/$tDb/vs$QDb
 cd $goldenPath/$tDb/vs$QDb
 ln -s $runDir/$tDb.$qDb.all.chain.gz .
 ln -s $runDir/README.txt .
@@ -1839,36 +1838,38 @@
   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${QDb}.bb" ) then
+    if ( "$tDb" !~ "GC*" ) 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
   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 \\
   | gzip -c > $tDb.$qDb.synNet.maf.gz
@@ -1885,36 +1886,38 @@
   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.$qDb.synNet.bb" ) then
+    if ( "$tDb" !~ "GC*" ) 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
+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
   sort -u md5sum.txt > tmp.sum