68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81
hiram
Tue Mar 31 12:08:22 2020 -0700
correct hub.txt not testHub.txt refs #23891
diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index d21d570..9402773 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -1,286 +1,293 @@
#!/usr/bin/env perl
use strict;
use warnings;
my $argc = scalar(@ARGV);
if ($argc != 3) {
printf STDERR "mkAsmStats Name asmName\n";
printf STDERR "e.g.: mkHubIndex Primates primates GCF_000001405.39_GRCh38.p13\n";
exit 255;
}
my $Name = shift;
my $asmHubName = shift;
my $defaultAssembly = shift;
my $home = $ENV{'HOME'};
my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
my $commonNameOrder = "$asmHubName.commonName.asmId.orderList.tsv";
my @orderList; # asmId of the assemblies in order from the *.list files
# the order to read the different .list files:
my $assemblyCount = 0;
my %betterName; # key is asmId, value is a common name better than found
# in assembly_report file
##############################################################################
# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
##############################################################################
sub commify($) {
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;
#
my $subSetMessage = "subset of $asmHubName only";
if ($asmHubName eq "vertebrate") {
$subSetMessage = "subset of other ${asmHubName}s only";
}
print <<"END"
$Name Genomes assembly hubs
Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
How to view the hub
-You can load this hub from our
-Public Hubs
-page or by clicking these assembly links to any of our official websites:
+Options:
+
+ - The links to the genome browser in the table below will attach that
+ one specific assembly to the genome browser. This is most likely what
+ you want.
+ - Instead, you can attach the entire set of assemblies as one group to
+ the genome browser with the following links depending upon which of
+ our mirror site browsers you prefer to use:
-
-
-
-To manually attach all the assemblies in this hub to other genome browsers:
+
+ - To manually attach all the assemblies in this hub to genome browsers
+ that are not one of the three UCSC mirror sites:
- -
- From the blue navigation bar, go to
+
- From the blue navigation bar, go to
My Data -> Track Hubs
- -
- Then select the My Hubs tab and enter this URL into the textbox:
+
- Then select the My Hubs tab and enter this URL into
+ the textbox:
https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt
- -
- Once you have added the URL to the entry form, press the Add Hub
- button to add the hub.
+ - 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
${Name} Hub Assembly dropdown menu.
Instead of adding all the assemblies in one collected group, use the individual
link to genome browser in the table below.
-
+
Data resource links
+
NOTE: Click on the column headers to sort the table by that column
-The link to genome browser will attach only that single assembly to
-the genome browser.
+The common name/link to genome browser will attach only that single assembly to
+the genome browser.
+The scientific name/and data download link provides access to the files for that one
+assembly hub.
+The other links provide access to NCBI resources for these assemblies.
+
END
} # sub startHtml()
##############################################################################
### start the table output
##############################################################################
sub startTable() {
print <<"END"
| count |
common name
link to genome browser |
scientific name
and data download |
NCBI assembly |
bioSample | bioProject |
assembly date,
source link |
|---|
END
} # sub startTable()
##############################################################################
### end the table output
##############################################################################
sub endTable() {
print <<"END"
END
} # sub endTable()
##############################################################################
### end the HTML output
##############################################################################
sub endHtml() {
if ($asmHubName ne "viral") {
- printf "\n
\n";
- printf "| Assembly hubs index pages: | \n";
+ printf "\n
\n\n";
}
print <<"END"