22a67b8eddff877e9265906cfbc4df5a41c3e0db
lrnassar
Mon Aug 5 12:01:54 2019 -0700
Pointing hard-coded links to hgdownload refs #23734
diff --git src/hg/makeDb/doc/VGP/mkHubIndex.pl src/hg/makeDb/doc/VGP/mkHubIndex.pl
index 8e61706..1ff0fff 100755
--- src/hg/makeDb/doc/VGP/mkHubIndex.pl
+++ src/hg/makeDb/doc/VGP/mkHubIndex.pl
@@ -1,248 +1,248 @@
#!/usr/bin/env perl
use strict;
use warnings;
my @orderList; # asmId of the assemblies in order from the *.list files
# the order to read the different .list files:
my @classList = qw( mammal bird reptile amphibian fish );
my %class; # key is asmId, value is from class list
my $assemblyCount = 0;
my %betterName; # key is asmId, value is common name
##############################################################################
# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
##############################################################################
sub commify($) {
my $text = reverse $_[0];
$text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $text
}
##############################################################################
### start the HTML output
##############################################################################
sub startHtml() {
my $timeStamp = `date "+%F"`;
chomp $timeStamp;
#
print <<"END"
VGP - Vertebrate Genomes Project assembly hub
This assembly hub contains assemblies released
by the
Vertebrate Genomes Project.
How to view the hub
You can load this hub from our
Public Hubs
page or by clicking these links to any of our official websites:
To manually attach this hub to other genome browsers:
-
From the blue navigation bar, go to
My Data -> Track Hubs
-
Then select the My Hubs tab and enter this URL into the textbox:
-
http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt
+
https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt
-
Once you have added the URL to the entry form, press the Add Hub
button to add the hub.
After adding the hub, you will be redirected to the gateway page. The
genome assemblies can be selected from the VGP Hub Assembly dropdown menu.
Data resource links
NOTE: Click on the column headers to sort the table by that column
END
}
##############################################################################
### start the table output
##############################################################################
sub startTable() {
print <<"END"
common name and
view in browser |
scientific name and
data download |
NCBI assembly |
bioSample | bioProject |
Taxon ID |
assembly date
VGP link |
class |
|---|
END
}
##############################################################################
### end the table output
##############################################################################
sub endTable() {
print <<"END"
END
}
##############################################################################
### end the HTML output
##############################################################################
sub endHtml() {
print <<"END"