f654134d5172e2687b3e6f98da7db78dd8379387
hiram
Tue Jan 21 15:01:57 2020 -0800
initial set of files to build "other vertebrates" assembly hub refs #2482
diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl
new file mode 100755
index 0000000..f598eb4
--- /dev/null
+++ src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl
@@ -0,0 +1,241 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $home = $ENV{'HOME'};
+my $Name = "Vertebrate";
+my $asmHubName = "vertebrate";
+my $srcDocDir = "${asmHubName}sAsmHub";
+my $asmHubDocDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+my $defaultAssembly = "GCF_000281125.3_ASM28112v4"; # Alligator_mississippiensis
+
+my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+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 $assemblyCount = 0;
+
+##############################################################################
+# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters:
+##############################################################################
+sub commify($) {
+ 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 $timeStamp;
+
+#
+
+print <<"END"
+
+
+
+
+
+
+$Name Genomes assembly hubs
+
+Assemblies from NCBI/Genbank/Refseq sources, subset of other ${asmHubName}s only.
+
+
+How to view the hub
+
+You can load this hub from our
+Public Hubs
+page or by clicking these assembly links to any of our official websites:
+
+
+
+
+To manually attach all the assemblies in this hub to other genome browsers:
+
+ -
+ From the blue navigation bar, go to
+ My Data -> Track Hubs
+ -
+ Then select the My Hubs tab and enter this URL into the textbox:
+
https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt
+ -
+ Once you have added the URL to the entry form, press the Add Hub
+ button to add the hub.
+
+
+
+
+After adding the hub, you will be redirected to the gateway page. The
+genome assemblies can be selected from the
+${Name}s 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.
+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() {
+print <<"END"
+
+
+
+
+