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/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl
index d849f5a..d4e1ef6 100755
--- src/hg/makeDb/doc/asmHubs/trackData.pl
+++ src/hg/makeDb/doc/asmHubs/trackData.pl
@@ -39,30 +39,32 @@
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
# assembly_report
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 $text
@@ -176,30 +178,51 @@
HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics
This assembly hub contains assemblies released
by the
Human Pangenome Reference Consortium.
END
+ } elsif ($brcIndex) {
+ print <<"END";
+
+
+
+
+
+
+BRC - Bioinformatics Research Center - track statistics
+
+
+
+
+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:
+brc-analytics.org
+
+
+END
} else {
print <<"END"
$Name Genomes assembly hubs, track statistics
Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
END
}