c44435c2093a2967aa189ef7394595edcc7cbf3d hiram Wed Mar 15 21:25:07 2023 -0700 adding viral and bacteria index pointers no redmine diff --git src/hg/makeDb/doc/asmHubs/hubIndex.pl src/hg/makeDb/doc/asmHubs/hubIndex.pl index 2115fa2..fe7e099 100755 --- src/hg/makeDb/doc/asmHubs/hubIndex.pl +++ src/hg/makeDb/doc/asmHubs/hubIndex.pl @@ -1,193 +1,205 @@ #!/usr/bin/env perl use strict; use warnings; use File::Basename; my $thisMachine = `uname -n`; chomp $thisMachine; if ($thisMachine ne "hgdownload") { + if ($thisMachine ne "hgdownload1") { + if ($thisMachine ne "hgdownload1.soe.ucsc.edu") { printf STDERR "# NOTE: This script is only used on hgdownload\n"; exit 255; } + } +} ############################################################################# sub startHtml() { printf '<!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="GenArk: UCSC Genome Archive" --> <!--#set var="ROOT" value=".." --> <!--#include virtual="$ROOT/inc/gbPageStartHardcoded.html" --> <h1>GenArk: UCSC Genome Archive</h1> ' } ############################################################################# sub endHtml() { printf ' </div><!-- closing gbsPage from gbPageStartHardcoded.html --> </div><!-- closing container-fluid from gbPageStartHardcoded.html --> <!--#include virtual="$ROOT/inc/gbFooterHardcoded.html"--> <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/sorttable.js"></script> <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/analytics.js"></script> </body></html> ' } ############################################################################# startHtml; my %expectedList = ( "VGP" => 1, "birds" => 1, "fish" => 1, "globalReference" => 1, "mammals" => 1, "primates" => 1, "vertebrate" => 1, "invertebrate" => 1, "fungi" => 1, "legacy" => 1, "plants" => 1, + "viral" => 1, + "bacteria" => 1, ); my %titles = ( "VGP" => "Vertebrate Genomes Project collection", "birds" => "NCBI bird genomes", "fish" => "NCBI fish genomes", "globalReference" => "Global Human Reference genomes, January 2020", "mammals" => "NCBI mammal genomes", "primates" => "NCBI primate genomes", "vertebrate" => "NCBI other vertebrate genomes", "invertebrate" => "NCBI invertebrate genomes", "fungi" => "NCBI fungi genomes", "legacy" => "NCBI genomes legacy/superseded by newer versions", "plants" => "NCBI plant genomes", + "viral" => "NCBI virus genomes", + "bacteria" => "NCBI bacteria genomes", "gtexAnalysis" => "Genotype-Tissue Expression (GTEx) Project analysis results track hub, V6 October 2015", "gtex" => "Genotype-Tissue Expression (GTEx) RNA-seq signal track hub, V6 October 2015", "mouseStrains" => "16 mouse strain assembly and track hub, May 2017", "neuroDiffCrispr" => "Structurally conserved primate cerebral cortex lincRNAs track hub, December 2018", ); my %otherTopLevels = ( "GCA" => 1, "GCF" => 1, "gtex" => 1, "gtexAnalysis" => 1, "mouseStrains" => 1, "neuroDiffCrispr" => 1, "UCSC_GI.assemblyHubList.txt" => 1, "index.html" => 1, ); my @orderOutHubs = ( "primates", "mammals", "birds", "fish", "vertebrate", "invertebrate", "fungi", "plants", + "viral", + "bacteria", "VGP", "globalReference", "mouseStrains", "legacy", ); my @orderOutTracks = ( "gtexAnalysis", "gtex", "neuroDiffCrispr", ); my %indexPage = ( "primates" => "index.html", "mammals" => "index.html", "birds" => "index.html", "fish" => "index.html", "vertebrate" => "index.html", "invertebrate" => "index.html", "fungi" => "index.html", "legacy" => "index.html", "plants" => "index.html", + "viral" => "index.html", + "bacteria" => "index.html", "VGP" => "index.html", "mouseStrains" => "hubIndex.html", "globalReference" => "index.html", "gtexAnalysis" => "index.html", "gtex" => "index.html", "neuroDiffCrispr" => "index.html", ); # verify all known directories and files, alert for any new ones open (FH, "ls -d /mirrordata/hubs/*|") or die "can not ls -d /mirrordata/hubs/*"; while (my $dirPath = <FH>) { chomp $dirPath; my $fileDirName = basename($dirPath); if (! (defined($expectedList{$fileDirName}) || defined($otherTopLevels{$fileDirName})) ) { printf STDERR "# something new: %s\n", $fileDirName; } } close (FH); ### Determine genome counts: my %genomeCounts; my $genomeCount = `grep -h ^genome /mirrordata/hubs/VGP/*enomes.txt | wc -l`; chomp $genomeCount; $genomeCounts{"VGP"} = $genomeCount; -my @checkList = ('primates', 'mammals', 'birds', 'fish', 'vertebrate', 'legacy', 'plants', "invertebrate", "fungi", 'globalReference'); +my @checkList = ('primates', 'mammals', 'birds', 'fish', 'vertebrate', 'legacy', 'plants', "invertebrate", "fungi", 'viral', 'bacteria', 'globalReference'); foreach my $hubSet (@checkList) { $genomeCount = `grep -h ^genome /mirrordata/hubs/$hubSet/genomes.txt | wc -l`; chomp $genomeCount; $genomeCounts{$hubSet} = $genomeCount; } my $hubCount = 0; printf "<table class='sortable' border='1'>\n"; printf "<thead><tr>\n"; printf " <th>hub gateway</th>\n"; printf " <th>description</th>\n"; printf "</tr></thead><tbody>\n"; # construct table foreach my $orderUp (@orderOutHubs) { printf "<tr>\n"; ++$hubCount; if ($orderUp eq "fish") { printf " <td><a href='%s/%s' target=_blank>fishes</a></td>\n", $orderUp, $indexPage{$orderUp}; } else { printf " <td><a href='%s/%s' target=_blank>%s</a></td>\n", $orderUp, $indexPage{$orderUp}, $orderUp; } if (defined($genomeCounts{$orderUp})) { printf " <td>%s (%d assemblies)</td>\n", $titles{$orderUp}, $genomeCounts{$orderUp}; } else { printf " <td>%s</td>\n", $titles{$orderUp}; } printf "</tr>\n"; } printf "</tbody></table>\n"; my $totalAsmHubs = `grep -v "^#" /mirrordata/hubs/UCSC_GI.assemblyHubList.txt | wc -l`; chomp $totalAsmHubs; printf "<p>\n"; printf "Please note: text file <a href='UCSC_GI.assemblyHubList.txt' target=_blank>listing</a> of %d NCBI/VGP genome assembly hubs\n", $totalAsmHubs; printf "</p>\n"; printf "<p>\n"; printf "Please note, the <em>invertebrate</em> category contains more than just <em>invertebrate</em> animals. Until these clades are sorted out, with extra categories created, you will also find parasites, protozoa, and other single celled eukaryotes in the <em>invertebrate</em> grouping.\n"; printf "</p>\n"; printf "<p>\n"; -printf "Please use the <a href='https://genome.ucsc.edu/assemblyRequest.html' target=_blank>Assembly Request</a> page to find and request GenBank assemblies that have not yet been included in the collections here.\n"; +printf "Please use the <a href='https://genome.ucsc.edu/assemblyRequest.html?all' target=_blank>Assembly Request</a> page to find and request GenBank assemblies that have not yet been included in the collections here.\n"; printf "</p>\n"; endHtml;