32029e8336069dd159be8945e30c6d9e9d9f3c98
hiram
  Mon Aug 31 15:09:33 2020 -0700
construct symLinks into goldenPath for GTF file and archive files refs #26415

diff --git src/hg/utils/automation/doEnsGeneUpdate.pl src/hg/utils/automation/doEnsGeneUpdate.pl
index b10009f..e84355b 100755
--- src/hg/utils/automation/doEnsGeneUpdate.pl
+++ src/hg/utils/automation/doEnsGeneUpdate.pl
@@ -265,31 +265,31 @@
 # there are too many things to check to verify identical to previous
 $identicalToPrevious = 0;
 
   $bossScript->add(<<_EOF_
 export db="$db"
 
 genePredToGtf -utr file process/\$db.allGenes.gp.gz stdout | gzip -c > process/\$db.ensGene.v$ensVersion.gtf.gz
 
 _EOF_
 	  );
 
   if ($dbExists && $identicalToPrevious ) {
       $bossScript->add(<<_EOF_
 hgsql -e 'INSERT INTO trackVersion \\
     (db, name, who, version, updateTime, comment, source, dateReference) \\
-    VALUES("\$db", "ensGene", "$ENV{'USER'}", "$ensVersion", now(), \\
+    VALUES("$db", "ensGene", "$ENV{'USER'}", "$ensVersion", now(), \\
 	"identical to previous version $previousEnsVersion", \\
 	"identical to previous version $previousEnsVersion", \\
 	"$ensVersionDateReference" );' hgFixed
 featureBits \$db ensGene > fb.\$db.ensGene.txt 2>&1
 _EOF_
 	  );
   } else {
       my $skipInv = "";
       $skipInv = "-skipInvalid" if (defined $skipInvalid);
 
       if ($opt_vegaGene) {
       $bossScript->add(<<_EOF_
 hgLoadGenePred $skipInv -genePredExt \$db \\
     vegaGene process/not.vegaPseudo.gp.gz >& load.not.pseudo.errors.txt
 hgLoadGenePred $skipInv -genePredExt \$db \\
@@ -392,41 +392,41 @@
     exit 255
 fi
 _EOF_
       );
       }
       if ($dbExists && ! $opt_vegaGene && defined $knownToEnsembl) {
 	  $bossScript->add(<<_EOF_
 hgMapToGene \$db ensGene knownGene knownToEnsembl
 _EOF_
 	  );
       }
       if ($opt_vegaGene) {
       $bossScript->add(<<_EOF_
 hgsql -e 'INSERT INTO trackVersion \\
     (db, name, who, version, updateTime, comment, source, dateReference) \\
-    VALUES("\$db", "vegaGene", "$ENV{'USER'}", "$ensVersion", now(), \\
+    VALUES("$db", "vegaGene", "$ENV{'USER'}", "$ensVersion", now(), \\
 	"with peptides $ensPepFile", \\
 	"$ensGtfUrl", \\
 	"$ensVersionDateReference" );' hgFixed
 _EOF_
       );
       } elsif ($dbExists) {
       $bossScript->add(<<_EOF_
 hgsql -e 'INSERT INTO trackVersion \\
     (db, name, who, version, updateTime, comment, source, dateReference) \\
-    VALUES("\$db", "ensGene", "$ENV{'USER'}", "$ensVersion", now(), \\
+    VALUES("$db", "ensGene", "$ENV{'USER'}", "$ensVersion", now(), \\
 	"with peptides $ensPepFile", \\
 	"$ensGtfUrl", \\
 	"$ensVersionDateReference" );' hgFixed
 featureBits \$db ensGene > fb.\$db.ensGene.txt 2>&1
 _EOF_
       );
       }
   }
   $bossScript->execute() if (! $opt_debug);
 } # doLoad
 
 #########################################################################
 # * step: process [dbHost]
 sub doProcess {
   my $runDir = "$buildDir/process";
@@ -685,31 +685,31 @@
 
   my $whatItDoes = "Create symlinks to make gtf files appear in goldenPath.";
   my $gpGeneDir = "$HgAutomate::goldenPath/$db/bigZips/genes";
   my $gpArchiveDir = "$HgAutomate::goldenPath/archive/$db/ensGene";
   my $bossScript = newBash HgRemoteScript("$runDir/doGoldenPath.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   &HgAutomate::mustMkdir($gpGeneDir);
   &HgAutomate::mustMkdir($gpArchiveDir);
 
   $bossScript->add(<<_EOF_
 export db="$db"
 rm -f $gpArchiveDir/\$db.ensGene.v$ensVersion.gtf.gz
 rm -f $gpArchiveDir/\$db.ensGene.v$ensVersion.genePred.gz
 ln -s `pwd`/process/\$db.ensGene.v$ensVersion.gtf.gz  $gpArchiveDir/
-ln -s `pwd`/process/\$db.allGenes.genePred.gz  $gpArchiveDir/\$db.ensGene.v$ensVersion.genePred.gz
+ln -s `pwd`/process/\$db.allGenes.gp.gz  $gpArchiveDir/\$db.ensGene.v$ensVersion.genePred.gz
 rm -f $gpGeneDir/\$db.ensGene.gtf.gz
 ln -s `pwd`/process/\$db.ensGene.v$ensVersion.gtf.gz  $gpGeneDir/\$db.ensGene.gtf.gz
 _EOF_
 	  );
 
   $bossScript->execute() if (! $opt_debug);
 } # doGoldenPath
 
 #########################################################################
 # * step: makeDoc [dbHost]
 sub doMakeDoc {
   my $runDir = "$buildDir";
   my $whatItDoes = "Display the make doc text to stdout.";
 
   if (! $dbExists) {