src/hg/makeDb/doc/asmHubs/mkAsmStats.pl 730f1cb766d7ab79175fc0c27f88e8139cdb9a60

730f1cb766d7ab79175fc0c27f88e8139cdb9a60
hiram
  Fri Sep 20 12:05:47 2024 -0700
customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337

diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
index c98b5e3..5f4e598 100755
--- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
+++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
@@ -24,30 +24,32 @@
 my $Name = shift;
 my $asmHubName = shift;
 my $inputList = shift;
 my $orderList = $inputList;
 if ( ! -s "$orderList" ) {
   $orderList = $toolsDir/$inputList;
 }
 
 my @orderList;	# asmId of the assemblies in order from the orderList file
 my %commonName;	# key is asmId, value is a common name, perhaps more appropriate
                 # than found in assembly_report file
 my $vgpIndex = 0;
 $vgpIndex = 1 if ($Name =~ m/vgp/i);
 my $hprcIndex = 0;
 $hprcIndex = 1 if ($Name =~ m/hprc/i);
+my $brcIndex = 0;
+$brcIndex = 1 if ($Name =~ m/brc/i);
 
 my $assemblyTotal = 0;	# complete list of assemblies in this group
 my $asmCount = 0;	# count of assemblies completed and in the table
 my $overallNucleotides = 0;
 my $overallSeqCount = 0;
 my $overallGapSize = 0;
 my $overallGapCount = 0;
 
 ##############################################################################
 # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
 ##############################################################################
 sub commify($) {
     my $text = reverse $_[0];
     $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
     return scalar reverse $text
@@ -101,30 +103,51 @@
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>VGP - Human Pangenome Reference Consortium assembly hubs, assembly statistics</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
+  } elsif ($brcIndex) {
+    print <<"END";
+<!DOCTYPE HTML>
+<!--#set var="TITLE" value="BRC - Bioinformatics Research Center - assembly statistics" -->
+<!--#set var="ROOT" value="../.." -->
+
+<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
+
+<h1>BRC - Bioinformatics Research Center - assembly statistics</h1>
+<p>
+<a href='https://brc-analytics.org/' target=_blank>
+<img src='BRClogo.svg' height=26 alt='BRC logo'></a></p>
+<p>
+This site will provide data access to genomes and annotations for all
+eukaryotic pathogens, host taxa, and vectors previously served by
+VEuPathDB. This is a part of the BRC Analytics project funded by the NIAID.
+For more information, see also:
+<a href=' https://brc-analytics.org' target=_blank>brc-analytics.org</a>
+</p>
+
+END
   } else {
     print <<"END"
 <!DOCTYPE HTML>
 <!--#set var="TITLE" value="$Name genomes assembly hubs, assembly statistics" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>$Name Genomes assembly hubs, assembly statistics</h1>
 <p>
 Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 END
   }