8edeca715fd909f21ec673b9e879788da8f44d6c
hiram
  Thu Feb 13 12:49:57 2020 -0800
beginning to add version 99 definitions and allow the process to skip download step already done refs #24963

diff --git src/hg/utils/automation/doEnsGeneUpdate.pl src/hg/utils/automation/doEnsGeneUpdate.pl
index 9e3b7cb..a6a6445 100755
--- src/hg/utils/automation/doEnsGeneUpdate.pl
+++ src/hg/utils/automation/doEnsGeneUpdate.pl
@@ -549,35 +549,40 @@
       }
       $bossScript->add(<<_EOF_
 grep -v "^#" infoOut.txt | awk '{printf "%s\\t%s,%s,%s,%s,%s\\n", \$1,\$2,\$3,\$8,\$9,\$10}' > $db.ensGene.nameIndex.txt
 ixIxx $db.ensGene.nameIndex.txt $db.ensGene.name.ix $db.ensGene.name.ixx
 
 _EOF_
 	  );
       }
   $bossScript->execute() if (! $opt_debug);
 } # doProcess
 
 #########################################################################
 # * step: download [dbHost]
 sub doDownload {
   my $runDir = "$buildDir/download";
-  # First, make sure we're starting clean.
+  # check if been already done
+  if (-s "$runDir/$ensGtfFile" && -s "$runDir/$ensPepFile" ) {
+     &HgAutomate::verbose(1,
+         "# step download is already completed, continuing...\n");
+     return;
+  }
+  # If not already done, then it should be clean.
   if (-d "$runDir" && ! $opt_debug) {
-    die "ERROR: download: looks like this was run successfully already\n" .
-      "($runDir exists)\nEither run with -continue=process or some later\n" .
-	"stage, or move aside/remove\n$runDir\nand run again.\n";
+    die "ERROR: download: looks like this was attempted unsuccessfully" .
+      " before.\n($runDir exists, download files do not)\n";
   }
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "download data from Ensembl FTP site.";
   my $bossScript = new HgRemoteScript("$runDir/doDownload.csh", $dbHost,
 				      $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 wget --tries=2 --user=anonymous --password=ucscGenomeBrowser\@ucsc.edu \\
 $ensGtfUrl \\
 -O $ensGtfFile
 wget --tries=2 --user=anonymous --password=ucscGenomeBrowser\@ucsc.edu \\
 $ensPepUrl \\
 -O $ensPepFile
 _EOF_