89cf9546eeccf2c5d1d519943114bf86bf280306
hiram
  Mon May 17 12:50:23 2021 -0700
better location for download files for assembly hub results no redmine

diff --git src/hg/utils/automation/doRecipBest.pl src/hg/utils/automation/doRecipBest.pl
index b575d7a..68d6f5d 100755
--- src/hg/utils/automation/doRecipBest.pl
+++ src/hg/utils/automation/doRecipBest.pl
@@ -332,38 +332,43 @@
 description of NET format:
     http://genome.ucsc.edu/goldenPath/help/net.html
 
 _EOF_
   ;
   close($fh);
 } # makeRbestReadme
 
 sub doDownload {
   return if ($opt_skipDownload);
   my $runDir = "$buildDir/axtChain";
   my $whatItDoes = "It makes a download (sub)dir.";
   my $bossScript = new HgRemoteScript("$runDir/doRBDownload.csh", $dbHost,
 				      $runDir, $whatItDoes);
 
-  my $downloadDir = "$HgAutomate::goldenPath/$tDb/vs$QDb";
+  my $goldenPath = $HgAutomate::goldenPath;
+  if ($tDb =~ m/^GC/) {
+     $goldenPath = &HgAutomate::asmHubDownloadDir($tDb);
+  }
+  my $downloadDir = "$goldenPath/$tDb/vs$QDb";
   &HgAutomate::checkExistsUnlessDebug("recipBest", "download",
 				      "$runDir/$tDb.$qDb.rbest.net.gz",
 				      $downloadDir);
   my $readme = "$runDir/README.rbest.txt";
   &makeRbestReadme($readme);
 
   $bossScript->add(<<_EOF_
+rm -fr $downloadDir/reciprocalBest
 mkdir $downloadDir/reciprocalBest
 cd $downloadDir/reciprocalBest
 ln -s $runDir/*.rbest.*.gz .
 ln -s $runDir/md5sum.rbest.txt md5sum.txt
 ln -s $readme README.txt
 mkdir axtRBestNet
 ln -s $buildDir/axtRBestNet/*.axt.gz $buildDir/axtRBestNet/md5sum.txt axtRBestNet/
 _EOF_
   );
   $bossScript->execute();
 } # doDownload
 
 sub loadRBest {
   if (! $opt_load) {
     &HgAutomate::verbose(1, "# specify -load to perform load step\n");