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/asmHubAllGaps.pl src/hg/utils/automation/asmHubAllGaps.pl
index f0976c83574..290d096a31f 100755
--- src/hg/utils/automation/asmHubAllGaps.pl
+++ src/hg/utils/automation/asmHubAllGaps.pl
@@ -1,82 +1,82 @@
 #!/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 != 5) {
   printf STDERR "usage: asmHubAllGaps.pl asmId asmId.names.tab asmId.agp.gz hubUrl bbi/asmId > asmId.allGaps.html\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   asmId.agp.gz is AGP file for this assembly,\n";
   printf STDERR "and   hubUrl is the URL to this assembly directory for the AGP file.\n";
   printf STDERR "and   bbi/asmId is the path prefix to .allGaps.bb.\n";
   exit 255;
 }
 
 my $asmId = shift;
 my $namesFile = shift;
 my $agpFile = shift;
 my $agpFileBase = basename($agpFile);
 my $hubUrl = shift;
 my $bbiPrefix = shift;
 my $allGapsBbi = "$bbiPrefix.allGaps.bb";
 
 if ( ! -s $agpFile ) {
   printf STDERR "ERROR: can not find AGP file:\n\t'%s'\n", $agpFile;
   exit 255;
 }
 if ( ! -s $allGapsBbi ) {
   printf STDERR "ERROR: can not find allGaps bbi file:\n\t'%s'\n", $allGapsBbi;
   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;
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 This track shows all gaps (any sequence of N's) in the $assemblyDate $em${organism}$noEm/$asmId genome assembly.  Not all gaps were annotated in the AGP file, this track includes all sequences of N's in the assembly.
 </p>
 <p>
 Genome assembly procedures are covered in the NCBI
 <a href="https://www.ncbi.nlm.nih.gov/assembly/basics/"
 target=_blank>assembly documentation</a>.<BR>
 NCBI also provides
 <a href="https://www.ncbi.nlm.nih.gov/assembly/$ncbiAssemblyId"
 target="_blank">specific information about this assembly</a>.
 </p>
 <p>
 Any sequence of N's in the assembly is marked as a gap in this track.
 The standard gap track only shows the gaps as annotated in the AGP file:
 <a href="$hubUrl/$agpFileBase" target=_blank>$asmId.agp.gz</a><br>
 The NCBI document
 <a href="https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/"
 target=_blank>AGP Specification</a> describes the format of the AGP file.
 </p>
 <p>
 Gaps are represented as black boxes in this track.
 There is no information in this track about order or orientation
 of the contigs on either side of the gap.
 </p>
 <p>
 _EOF_
     ;
-my $gapCount = `bigBedInfo $allGapsBbi | egrep "itemCount:|basesCovered:" | xargs echo | sed -e 's/itemCount/gap count/; s/basesCovered/bases covered/;'`;
+my $gapCount = `/cluster/bin/x86_64/bigBedInfo $allGapsBbi | egrep "itemCount:|basesCovered:" | xargs echo | sed -e 's/itemCount/gap count/; s/basesCovered/bases covered/;'`;
 chomp $gapCount;
 printf "Gap count and coverage: %s</li>\n", $gapCount;
 
 printf "</p>\n";