730f1cb766d7ab79175fc0c27f88e8139cdb9a60 hiram Fri Sep 20 12:05:47 2024 -0700 customized text for index page on BRC project (these custom headers should instead be header.html in the project source directories) and now sending out assemblyList.json file refs #34337 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index e08ae56..529a5b3 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -26,33 +26,35 @@ my $Name = shift; my $asmHubName = shift; my $defaultAssembly = shift; my $inputList = shift; my $orderList = $inputList; if ( ! -s "$orderList" ) { $orderList = $toolsDir/$inputList; } my %cladeId; # value is asmId, value is clade, useful for 'legacy' index page printf STDERR "# mkHubIndex %s %s %s %s\n", $Name, $asmHubName, $defaultAssembly, $orderList; my $hprcIndex = 0; my $ccgpIndex = 0; my $vgpIndex = 0; +my $brcIndex = 0; $hprcIndex = 1 if ($Name =~ m/hprc/i); $ccgpIndex = 1 if ($Name =~ m/ccgp/i); $vgpIndex = 1 if ($Name =~ m/vgp/i); +$brcIndex = 1 if ($Name =~ m/brc/i); my %extraClass; # key is asmId, value is taxon 'class' as set by VGP project if ($vgpIndex || $ccgpIndex) { my $whichIndex = "vgp"; $whichIndex = "ccgp" if ($ccgpIndex); my $extraClass = "$home/kent/src/hg/makeDb/doc/${whichIndex}AsmHub/${whichIndex}.taxId.asmId.class.txt"; open (FH, "<$extraClass") or die "can not read $extraClass"; while (my $line = ) { my ($taxId, $asmId, $class) = split('\t', $line); $extraClass{$asmId} = $class; } close (FH); } my @orderList; # asmId of the assemblies in order from the *.list files # the order to read the different .list files: @@ -138,30 +140,54 @@

HPRC - Human Pangenome Reference Consortium assembly hub

This assembly hub contains assemblies released by the Human Pangenome Reference Consortium.

END + } elsif ($brcIndex) { + print <<"END"; + + + + + + +

BRC - Bioinformatics Research Center

+ +

+This site will provide data access to genomes and annotations for all +eukaryotic pathogens, host taxa, and vectors previously served by +VEuPathDB. This is a part of the BRC Analytics project funded by the NIAID. +For more information, see also: +brc-analytics.org. +Access this assembly data in + +JSON format. +

+ +END } else { print <<"END";

$Name Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.

END } @@ -397,31 +423,31 @@ chomp $bioSample; $ncbiFtpLink = "https://ftp.ncbi.nlm.nih.gov/genomes/all/$accessionDir/${accessionId}_${asmName}"; } my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId"; my $browserName = $commonName; my $browserUrl = "https://genome.ucsc.edu/h/$accessionId"; if ($asmId !~ m/^GC/) { $hubUrl = "https://hgdownload.soe.ucsc.edu/goldenPath/$asmId/bigZips"; $browserUrl = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$asmId"; $browserName = "$commonName ($asmId)"; } printf "%d\n", ++$rowCount; # common name and view in browser if ( $asmId =~ m/^GC/ ) { my $hubTxt = "${hubUrl}/hub.txt"; - my $igvUrl = "https://igv.org/app-test/?hubURL=$hubTxt"; + my $igvUrl = "https://igv.org/app/?hubURL=$hubTxt"; printf "%s[IGV]\n", $browserUrl, $browserName, $igvUrl; } else { printf "%s\n", $browserUrl, $browserName; } # scientific name and data download printf " %s\n", $hubUrl, $sciName; if ($asmId !~ m/^GC/) { printf " %s_%s\n", $gcPrefix, $asmAcc, $accessionId, $asmName; } else { printf " %s\n", $accessionId, $asmId; } # viruses do not appear to have BioSample if ($asmHubName ne "viral") { if ( $bioSample ne "notFound" ) { printf " %s\n", $bioSample, $bioSample;