b9f7ddc7bbae881dd79b74932bc6c94d26b94bdf hiram Mon May 10 11:47:23 2021 -0700 turning on dynamic blat for both hgwdev and the hgdownload files refs #26658 diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl index 056d735..a0465d9 100755 --- src/hg/makeDb/doc/asmHubs/mkGenomes.pl +++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl @@ -1,39 +1,39 @@ #!/usr/bin/env perl use strict; use warnings; use File::Basename; my $argc = scalar(@ARGV); if ($argc != 3) { printf STDERR "mkGenomes.pl blatHost blatPort [two column name list] > .../hub/genomes.txt\n"; - printf STDERR "e.g.: mkGenomes.pl blat-backup 4040 vgp.primary.assemblies.tsv > .../vgp/genomes.txt\n"; + printf STDERR "e.g.: mkGenomes.pl dynablat-01 4040 vgp.primary.assemblies.tsv > .../vgp/genomes.txt\n"; printf STDERR "e.g.: mkGenomes.pl hgwdev 4040 vgp.primary.assemblies.tsv > .../vgp/download.genomes.txt\n"; printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n"; printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n"; printf STDERR "column 2: common name for species, columns separated by tab\n"; printf STDERR "result will write a local asmId.genomes.txt file for each hub\n"; printf STDERR "and a local asmId.hub.txt file for each hub\n"; printf STDERR "and a local asmId.groups.txt file for each hub\n"; printf STDERR "and the output to stdout will be the overall genomes.txt\n"; printf STDERR "index file for all genomes in the given list\n"; exit 255; } my $downloadHost = "hgwdev"; -my @blatHosts = qw( blat-backup hgwdev ); +my @blatHosts = qw( dynablat-01 dynablat-01 ); my @blatPorts = qw( 4040 4040 ); ################### writing out hub.txt file, twice ########################## sub singleFileHub($$$$$$$$$$) { my ($fh1, $fh2, $accessionId, $orgName, $descr, $asmId, $defPos, $taxId, $trackDb, $accessionDir) = @_; my @fhN; push @fhN, $fh1; push @fhN, $fh2; my $fileCount = 0; my @tdbLines; open (TD, "<$trackDb") or die "can not read trackDb: $trackDb"; while (my $tdbLine = <TD>) { chomp $tdbLine; push @tdbLines, $tdbLine;