bdc5df573ffaa879405a4e13f10c205fed01c4d1
hiram
  Fri May 1 12:55:06 2026 -0700
explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811

diff --git src/hg/utils/automation/asmHubSimpleRepeat.pl src/hg/utils/automation/asmHubSimpleRepeat.pl
index 42d597e846f..05ffbecb16d 100755
--- src/hg/utils/automation/asmHubSimpleRepeat.pl
+++ src/hg/utils/automation/asmHubSimpleRepeat.pl
@@ -25,32 +25,32 @@
 my $chromSizes = "$buildDir/$asmId.chrom.sizes";
 
 if ( ! -s $trfBbi ) {
   printf STDERR "ERROR: can not find CpG masked file:\n\t'%s'\n", $trfBbi;
   exit 255;
 }
 
 my $em = "<em>";
 my $noEm = "</em>";
 my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`;
 chomp $assemblyDate;
 my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`;
 chomp $ncbiAssemblyId;
 my $organism = `grep -v "^#" $namesFile | cut -f5`;
 chomp $organism;
-my $itemCount = `bigBedInfo $trfBbi | egrep "itemCount:" | sed -e 's/itemCount: //;'`;
-my $basesCovered = `bigBedInfo $trfBbi | egrep "basesCovered:" | sed -e 's/basesCovered: //;'`;
+my $itemCount = `/cluster/bin/x86_64/bigBedInfo $trfBbi | egrep "itemCount:" | sed -e 's/itemCount: //;'`;
+my $basesCovered = `/cluster/bin/x86_64/bigBedInfo $trfBbi | egrep "basesCovered:" | sed -e 's/basesCovered: //;'`;
 chomp $itemCount;
 chomp $basesCovered;
 my $bases = $basesCovered;
 $bases =~ s/,//g;
 my $asmSize = &AsmHub::asmSize($chromSizes);
 my $percentCoverage = sprintf("%.2f", (100.0 * $bases) / $asmSize);
 $asmSize = &AsmHub::commify($asmSize);
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 This track displays simple tandem repeats (possibly imperfect repeats) on
 the $assemblyDate $em${organism}$noEm/$asmId/$ncbiAssemblyId genome assembly,
 located by <a href="http://tandem.bu.edu/trf/trf.submit.options.html" 
 target=_blank>Tandem Repeats