src/hg/makeDb/doc/asmHubs/mkHubIndex.pl cdd0101336b3399e8d1a204a298b017a2675cc3a

cdd0101336b3399e8d1a204a298b017a2675cc3a
hiram
  Fri Jan 24 10:35:41 2020 -0800
now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748

diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index b909465..11e8ae1 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -28,40 +28,45 @@
     my $text = reverse $_[0];
     $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
     return scalar reverse $text
 }
 
 ##############################################################################
 ### start the HTML output
 ##############################################################################
 sub startHtml() {
 
 my $timeStamp = `date "+%F"`;
 chomp $timeStamp;
 
 # <html xmlns="http://www.w3.org/1999/xhtml">
 
+my $subSetMessage = "subset of $asmHubName only";
+if ($asmHubName eq "vertebrate") {
+   $subSetMessage = "subset of other ${asmHubName}s only";
+}
+
 print <<"END"
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="$Name genomes assembly hubs" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>$Name Genomes assembly hubs</h1>
 <p>
-Assemblies from NCBI/Genbank/Refseq sources, subset of $asmHubName only.
+Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 <h3>How to view the hub</h3>
 <p>
 You can load this hub from our
 <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> 
 page or by clicking these assembly links to any of our official websites:
 <ul>
   <li>
     <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
     target="_blank">genome.ucsc.edu</a></li>
   <li> 
     <a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
     target="_blank">genome-euro.ucsc.edu</a></li>
   <li>
@@ -160,30 +165,31 @@
 
 ##############################################################################
 ### tableContents()
 ##############################################################################
 sub tableContents() {
   my $rowCount = 0;
   foreach my $asmId (@orderList) {
     my $accessionDir = substr($asmId, 0 ,3);
     $accessionDir .= "/" . substr($asmId, 4 ,3);
     $accessionDir .= "/" . substr($asmId, 7 ,3);
     $accessionDir .= "/" . substr($asmId, 10 ,3);
     $accessionDir .= "/" . $asmId;
     my $ncbiFtpLink = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$accessionDir/";
     my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir";
     my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
+    next if (! -s "$asmReport");
     my ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3);
     my $chromSizes="${buildDir}/${asmId}.chrom.sizes";
     my $sciName = "notFound";
     my $commonName = "notFound";
     my $bioSample = "notFound";
     my $bioProject = "notFound";
     my $taxId = "notFound";
     my $asmDate = "notFound";
     my $itemsFound = 0;
     open (FH, "<$asmReport") or die "can not read $asmReport";
     while (my $line = <FH>) {
       last if ($itemsFound > 5);
       chomp $line;
       $line =~ s/
//g;;
       $line =~ s/\s+$//g;;