31cfa0823734a570e9aabdbfd730dbd01f0b0a85
hiram
  Tue Apr 6 13:51:13 2021 -0700
eliminate the trailing ^M on the taxId and testing blat-backup refs #26658

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 7fa3282..056d735 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 localhost 4040 vgp.primary.assemblies.tsv > .../vgp/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 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( localhost hgwdev );
+my @blatHosts = qw( blat-backup hgwdev );
 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;
@@ -135,31 +135,31 @@
     next;
   }
   my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
   my $trackDb = "$buildDir/$asmId.trackDb.txt";
   if ( ! -s "${trackDb}" ) {
     printf STDERR "# %03d not built yet: %s\n", $orderKey, $asmId;
     printf STDERR "# '%s'\n", $trackDb;
     next;
   }
   if ( ! -s "${asmReport}" ) {
     printf STDERR "# %03d missing assembly_report: %s\n", $orderKey, $asmId;
     next;
   }
   ++$buildDone;
 printf STDERR "# %03d genomes.txt %s/%s\n", $buildDone, $accessionDir, $accessionId;
-  my $taxId=`grep -i "taxid:" $asmReport | head -1 | awk '{printf \$(NF)}'`;
+  my $taxId=`grep -i "taxid:" $asmReport | head -1 | awk '{printf \$(NF)}' | tr -d \$'\\r'`;
   chomp $taxId;
   my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
   chomp $descr;
   my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
   chomp $orgName;
   if (defined($commonName{$asmId})) {
      $orgName = $commonName{$asmId};
   }
 
   printf "genome %s\n", $accessionId;
   printf "taxId %s\n", $taxId if (length($taxId) > 1);
   printf "trackDb ../%s/%s/trackDb.txt\n", $accessionDir, $accessionId;
   printf "groups groups.txt\n";
   printf "description %s\n", $orgName;
   printf "twoBitPath ../%s/%s/%s.2bit\n", $accessionDir, $accessionId, $accessionId;