46f246dc334a47ded8a439de133f6d94ef9dae81
hiram
  Thu May 7 14:40:00 2026 -0700
now working correctly with UCSC database assemblies for pushing the lift.over file out to hgdownload refs #31811

diff --git src/hg/utils/otto/userRequests/chainNetTrackDb.pl src/hg/utils/otto/userRequests/chainNetTrackDb.pl
index 0930bf728a3..fd7c05f260f 100755
--- src/hg/utils/otto/userRequests/chainNetTrackDb.pl
+++ src/hg/utils/otto/userRequests/chainNetTrackDb.pl
@@ -62,53 +62,53 @@
   printf STDERR "ERROR: must be run from a build directory; no %s/ in cwd %s\n",
     $axtChain, getcwd();
   exit 255;
 }
 
 # normalize query - strip _asmName suffix for GenArk
 my $qAcc = $queryDb;
 if ($queryDb =~ /^(GC[AF]_\d+\.\d+)/) {
   $qAcc = $1;
 }
 my $Query = ucfirst($qAcc);
 
 ##############################################################################
 # look up target metadata from dbDb
 ##############################################################################
-my $tRow = `hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$targetDb"' hgcentraltest 2>/dev/null`;
+my $tRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$targetDb"' hgcentraltest 2>/dev/null`;
 chomp $tRow;
 if (length($tRow) < 1) {
   printf STDERR "ERROR: target db '%s' not found in hgcentraltest.dbDb\n", $targetDb;
   exit 255;
 }
 my ($tOrganism, $tSciName, $tTaxId, $tDesc) = split(/\t/, $tRow);
 $tOrganism = "" if (!defined $tOrganism);
 
 ##############################################################################
 # look up query metadata
 ##############################################################################
 my $qOrganism = "";
 my $qSciName  = "";
 my $qTaxId    = "";
 my $qDate     = "";
 my $qAsmName  = "";
 
 if ($qAcc =~ /^GC[AF]_/) {
   # GenArk: get commonName/scientificName/taxId/asmName from the genark
   # table; only fall back to assembly_report.txt for the assembly date,
   # which the genark table does not carry.
-  my $gRow = `hgsql -N -e 'SELECT commonName,scientificName,taxId,asmName FROM genark WHERE gcAccession="$qAcc"' hgcentraltest 2>/dev/null`;
+  my $gRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT commonName,scientificName,taxId,asmName FROM genark WHERE gcAccession="$qAcc"' hgcentraltest 2>/dev/null`;
   chomp $gRow;
   if (length($gRow) < 1) {
     printf STDERR "ERROR: GenArk accession '%s' not found in hgcentraltest.genark\n", $qAcc;
     exit 255;
   }
   ($qOrganism, $qSciName, $qTaxId, $qAsmName) = split(/\t/, $gRow);
   $qOrganism = "" if (!defined $qOrganism);
   $qSciName  = "" if (!defined $qSciName);
   $qTaxId    = "" if (!defined $qTaxId);
   $qAsmName  = "" if (!defined $qAsmName);
   # commonName may be empty; fall back to scientificName
   if (length($qOrganism) < 1) {
     $qOrganism = $qSciName;
   }
 
@@ -124,31 +124,31 @@
   chomp $asmReport;
   if (! -s $asmReport) {
     $asmReport = `ls -d $ncbiPath/${qAcc}*/${qAcc}*assembly_report.txt 2>/dev/null | head -1`;
     chomp $asmReport;
   }
   if (-s $asmReport) {
     my $ymd = `grep -i 'date:' $asmReport | head -1 | tr -d '\r' | sed -e 's/.*date: *//i;'`;
     chomp $ymd;
     if ($ymd =~ /^(\d{4})-(\d{1,2})/) {
       my ($y, $m) = ($1, $2 + 0);
       $qDate = sprintf("%s %d", $months[$m], $y) if ($m >= 1 && $m <= 12);
     }
   }
 } else {
   # UCSC native: dbDb has organism, sciName, taxId, description
-  my $qRow = `hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$qAcc"' hgcentraltest 2>/dev/null`;
+  my $qRow = `/cluster/bin/x86_64/hgsql -N -e 'SELECT organism,scientificName,taxId,description FROM dbDb WHERE name="$qAcc"' hgcentraltest 2>/dev/null`;
   chomp $qRow;
   if (length($qRow) < 1) {
     printf STDERR "ERROR: query db '%s' not found in hgcentraltest.dbDb\n", $qAcc;
     exit 255;
   }
   my $desc;
   ($qOrganism, $qSciName, $qTaxId, $desc) = split(/\t/, $qRow);
   $qOrganism = "" if (!defined $qOrganism);
   # dbDb.description is typically the assembly date string, e.g. "Apr. 2017"
   $qDate = defined($desc) ? $desc : "";
 }
 
 ##############################################################################
 # probe axtChain/ for available files
 ##############################################################################