src/hg/makeDb/doc/asmHubs/mkHubIndex.pl 790b166f17ba0ef2f8cfe220dbc6c2a67035ede9

790b166f17ba0ef2f8cfe220dbc6c2a67035ede9
hiram
  Wed Mar 15 21:16:40 2023 -0700
adding HPRC links to the index pages refs #30508

diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index 01e85af..b2d3fc7 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -23,31 +23,33 @@
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 my $Name = shift;
 my $asmHubName = shift;
 my $defaultAssembly = shift;
 my $inputList = shift;
 my $orderList = $inputList;
 if ( ! -s "$orderList" ) {
   $orderList = $toolsDir/$inputList;
 }
 my %cladeId;	# value is asmId, value is clade, useful for 'legacy' index page
 
 printf STDERR "# mkHubIndex %s %s %s %s\n", $Name, $asmHubName, $defaultAssembly, $orderList;
+my $hprcIndex = 0;
 my $vgpIndex = 0;
+$hprcIndex = 1 if ($Name =~ m/hprc/i);
 $vgpIndex = 1 if ($Name =~ m/vgp/i);
 my %vgpClass;	# key is asmId, value is taxon 'class' as set by VGP project
 if ($vgpIndex) {
   my $vgpClass = "$home/kent/src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt";
   open (FH, "<$vgpClass") or die "can not read $vgpClass";
   while (my $line = <FH>) {
     my ($taxId, $asmId, $class) = split('\t', $line);
     $vgpClass{$asmId} = $class;
   }
   close (FH);
 }
 
 my @orderList;	# asmId of the assemblies in order from the *.list files
 # the order to read the different .list files:
 my $assemblyTotal = 0;
@@ -94,44 +96,65 @@
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>VGP - Vertebrate Genomes Project assembly hub</h1>
 <p>
 <a href='https://vertebrategenomesproject.org/' target=_blank>
 <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p>
 <p>
 This assembly hub contains assemblies released
 by the <a href='https://vertebrategenomesproject.org/' target=_blank>
 Vertebrate Genomes Project.</a> $vgpSubset
 </p>
 
 END
 } else {
+  if ($hprcIndex) {
+    print <<"END";
+<!DOCTYPE HTML 4.01 Transitional>
+<!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium" -->
+<!--#set var="ROOT" value="../.." -->
+
+<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
+
+<h1>HPRC - Human Pangenome Reference Consortium assembly hub</h1>
+<p>
+<a href='https://humanpangenome.org/' target=_blank>
+<img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p>
+<p>
+This assembly hub contains assemblies released
+by the <a href='https://humanpangenome.org/' target=_blank>
+Human Pangenome Reference Consortium.</a>
+</p>
+
+END
+  } else {
     print <<"END";
 <!DOCTYPE HTML 4.01 Transitional>
 <!--#set var="TITLE" value="$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, $subSetMessage.
 </p>
 
 END
   }
+}
 
 print <<"END";
 <h3>How to view the hub</h3>
 <p>
 Options:
 <ol>
   <li>The links to the genome browser in the table below will attach that
       one specific assembly to the genome browser.  This is most likely what
       you want.  Alternatively, the entire set of assemblies can be attached
       as one group to the genome browser with the following links depending
       upon which of our mirror site browsers you prefer to use:
 <table border="1">
 <tr>
   <th>attach all assemblies to selected site:</th>
   <th>&nbsp;</th>