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
@@ -1,100 +1,100 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 3) {
   printf STDERR "usage: asmHubSimpleRepeat.pl asmId asmId.names.tab buildDir\n";
   printf STDERR "where asmId is the assembly identifier,\n";
   printf STDERR "and   asmId.names.tab is naming file for this assembly,\n";
   printf STDERR "and buildDir is the directory with bbi/asmId.simpleRepeats.bb\n";
   printf STDERR "    and the asmId.chrom.sizes\n";
   exit 255;
 }
 
 my $asmId = shift;
 my $namesFile = shift;
 my $buildDir = shift;
 my $trfBbi = "$buildDir/bbi/$asmId.simpleRepeat.bb";
 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
 Finder</a> (TRF) which is specialized for this purpose. These repeats can
 occur within coding regions of genes and may be quite
 polymorphic. Repeat expansions are sometimes associated with specific
 diseases.</p>
 
 There are $itemCount items in the track covering $basesCovered bases,
 assembly size $asmSize bases, percent coverage % $percentCoverage.
 
 <h2>Methods</h2>
 <p>
 For more information about the TRF program, see Benson (1999).
 </p>
 
 <h2>Credits</h2>
 <p>
 TRF was written by
 <a href="http://tandem.bu.edu/benson.html" target=_blank>Gary Benson</a>.</p>
 
 <h2>References</h2>
 
 <p>
 Benson G.
 <a href="http://nar.oxfordjournals.org/content/27/2/573.abstract" target="_blank">
 Tandem repeats finder: a program to analyze DNA sequences</a>.
 <em>Nucleic Acids Res</em>. 1999 Jan 15;27(2):573-80.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9862982" target="_blank">9862982</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217/" target="_blank">PMC148217</a>
 </p>
 <h2>Credits</h2>
 
 <p>This track was generated using a modification of a program developed by G. Miklem and L. Hillier 
 (unpublished).</p>
 
 <h2>References</h2>
 
 <p>
 Gardiner-Garden M, Frommer M.
 <a href="http://www.sciencedirect.com/science/article/pii/0022283687906899" target="_blank">
 CpG islands in vertebrate genomes</a>.
 <em>J Mol Biol</em>. 1987 Jul 20;196(2):261-82.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/3656447" target="_blank">3656447</a>
 </p>
 _EOF_
    ;