1b17e173bde7713fe7080825f27efb8e952419f4
hiram
  Thu Aug 1 14:51:39 2019 -0700
updating text after QA comments refs #23734

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index 369fa77..b10adda 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -1,24 +1,26 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 use File::Basename;
 
+my $sourceServer = "hgdownload.soe.ucsc.edu";
+
 my @months = qw( 0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec );
 
 sub usage() {
   printf STDERR "usage: asmHubGatewayPage.pl <pathTo>/*assembly_report.txt <pathTo>/asmId.chrom.sizes <pathTo>/image.jpg <pathTo>/photoCredits.txt\n";
   printf STDERR "output is to stdout, redirect to file: > description.html\n";
   printf STDERR "photoCredits.txt is a two line tag<tab>string file:\n";
   printf STDERR "tags: photoCreditURL and photoCreditName\n";
   printf STDERR "use string 'noPhoto' for image and credits when no photo\n";
   exit 255;
 }
 
 sub chromSizes($) {
   my ($sizeFile) = @_;
   if ( -s $sizeFile ) {
     printf STDERR "# reading chrom.sizes file:\n#\t'%s\'\n", $sizeFile;
@@ -275,68 +277,74 @@
     target=_blank>
     <img src=\"../hubs/ncbiAssemblies/%s/html/%s\" width=%d height=%d alt=\"%s\"></a>
   </td></tr>
   <tr><td align=right>
     <font size=-1> <em>%s</em><BR>
     </font>
     <font size=-2> (Photo courtesy of
       <a href=\"%s\" target=_blank>%s</a>)
     </font>
   </td></tr>
 </table>
 \n", $imageWidth+$imageWidthBorder, $imageHeight, $asmAccession, $ftpName, $imageName, $imageWidth, $imageHeight, $commonName, $orgName, $photoCreditURL, $photoCreditName;
 }
 
 printf "<p>
-<b>Common name: %s</b><br>
+<b>Common name:</b>&nbsp;%s<br>
 <b>Taxonomic name: %s, taxonomy ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s\" target=_\"_blank\"> %s</a><br>
 <b>Sequencing/Assembly provider ID:</b> %s<br>
 <b>Assembly date:</b> %s<br>
 <b>Assembly type:</b> %s<br>
 <b>Assembly level:</b> %s<br>
 <b>Biosample:</b> <a href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=%s\" target=\"_blank\">%s</a><br>
 <b>Assembly accession ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=\"_blank\">%s</a><br>
 <b>Assembly FTP location:</b> <a href=\"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/%s\" target=\"_blank\">%s</a><br>
 \n", $commonName, $orgName, $taxId, $taxId, $submitter, $asmDate, $descrAsmType,
   $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $urlDirectory, $urlDirectory;
 
 chromSizes($chromSizes);
 
 printf "</p>\n<hr>
 <p>
 <b>Download files for this assembly hub:</b><br>
 To use the data from this assembly for a local hub instance at your
 institution, download these data as indicated by these instructions.<br>
-See also: <a href=\"/goldenPath/help/hgTrackHubHelp.html\" target=_blank>track hub help</a> documentation.<br>
+See also: <a href='/goldenPath/help/hgTrackHubHelp.html' target=_blank>track hub help</a> documentation.<br>
 <br>
-To download these data, issue this <em>wget</em> command:
+To download this assembly data, use this <em>rsync</em> command:
 <pre>
-wget --timestamping -m -nH -x --cut-dirs=5 -e robots=off -np -k \\
+  rsync -a -P rsync://$sourceServer/hubs/VGP/genomes/$asmId/ ./$asmId/
+
+  which creates the local directory: ./$asmId/
+</pre>
+or this <em>wget</em> command:
+<pre>
+  wget --timestamping -m -nH -x --cut-dirs=4 -e robots=off -np -k \\
     --reject \"index.html*\" -P \"$asmId\" \\
-       http://genome-test.soe.ucsc.edu/hubs/ncbiAssemblies/$asmId/
+       http://$sourceServer/hubs/VGP/genomes/$asmId/
+
+  which creates a local directory: ./$asmId/
 </pre>
-to download the files for this assembly,<br>
-creating the local directory: \"$asmId\"<br>
 <br>
 There is an included $asmId.genomes.txt file in that download
 data to use for your local track hub instance.<br>
 You will need to add a hub.txt file to point to this genomes.txt file.<br>
 Something like:
 <pre>
 hub myLocalHub
 shortLabel myLocalHub
-longLabel genomes from RefSeq assemblies
+longLabel genomes from Vertebrate Genomes Project assemblies
 genomesFile $asmId.genomes.txt
 email yourEmail\@yourdomain.edu
 descriptionUrl html/$asmId.description.html
 </pre>
 The <em>html/$asmId.description.html</em> page is information for your users to
 describe this assembly.  This WEB page with these instructions
 is an instance of html/$asmId.description.html file.
 </p>\n";
 
 printf "<hr>
 <p>
 To operate a blat server on this assembly, in the directory where you have
 the $asmId.2bit file:
 <pre>
 gfServer -log=%s.gfServer.trans.log -ipLog -canStop start \\