8b6ee6734404f7ab681577f5044559dd2ce8bc08
hiram
Fri Sep 3 12:24:45 2021 -0700
print heredoc need to have ; on the print line refs #23891
diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index 46f1ad0..dfefd04 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -73,65 +73,65 @@
my $subSetMessage = "subset of $asmHubName only";
if ($asmHubName eq "vertebrate") {
$subSetMessage = "subset of other ${asmHubName}s only";
}
if ($vgpIndex) {
my $vgpSubset = "(set of primary assemblies)";
if ($orderList =~ m/vgp.alternate/) {
$vgpSubset = "(set of alternate/haplotype assemblies)";
} elsif ($orderList =~ m/vgp.trio/) {
$vgpSubset = "(set of trio assemblies, maternal/paternal)";
} elsif ($orderList =~ m/vgp.legacy/) {
$vgpSubset = "(set of legacy/superseded assemblies)";
}
- print <<"END"
+ print <<"END";
VGP - Vertebrate Genomes Project assembly hub
This assembly hub contains assemblies released
by the
Vertebrate Genomes Project. $vgpSubset
END
} else {
- print <<"END"
+ print <<"END";
$Name Genomes assembly hubs
Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
END
}
-print <<"END"
+print <<"END";
How to view the hub
Options:
- 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:
| attach all assemblies to selected site: |
|
genome.ucsc.edu |
@@ -162,61 +162,71 @@
After adding the hub, you will be redirected to the gateway page. The
genome assemblies can be selected from the
${Name} Hub Assembly dropdown menu.
Instead of adding all the assemblies in one collected group, use the individual
view in browser in the table below.
Data resource links
NOTE: Click on the column headers to sort the table by that column
The common name and view in browser will attach only that single assembly to
the genome browser.
The scientific name and data download link provides access to the files for that one
assembly hub.
+END
+
+ if ($vgpIndex) {
+ print <<"END";
The class VGP link provides access to the VGP GenomeArk page for that genome.
+END
+
+ }
+
+print <<"END";
The other links provide access to NCBI resources for these assemblies.
END
+
} # sub startHtml()
##############################################################################
### start the table output
##############################################################################
sub startTable() {
print '
| count |
common name and
view in browser |
scientific name
and data download |
NCBI assembly |
BioSample | BioProject |
assembly date,
source link |
';
if ($vgpIndex) {
printf "class
VGP link | \n";
}
print "
|---|
\n";
} # sub startTable()
##############################################################################
### end the table output
##############################################################################
sub endTable() {
-print <<"END"
+print <<"END";
END
} # sub endTable()
##############################################################################
### end the HTML output
##############################################################################
sub endHtml() {
&commonHtml::otherHubLinks($vgpIndex, $asmHubName);
&commonHtml::htmlFooter($vgpIndex, $asmHubName);
} # sub endHtml()