24891487d4c04f503b44631ea97773e8a2071b56 hiram Fri May 1 12:39:24 2026 -0700 explicit path names to allow these scripts to work on cron jobs refs #31811 diff --git src/hg/utils/automation/asmHubGc5Percent.pl src/hg/utils/automation/asmHubGc5Percent.pl index 6674c10b52f..8a088c85ed1 100755 --- src/hg/utils/automation/asmHubGc5Percent.pl +++ src/hg/utils/automation/asmHubGc5Percent.pl @@ -22,31 +22,31 @@ my $gc5Bw = "$buildDir/bbi/$asmId.gc5Base.bw"; if ( ! -s $gc5Bw ) { printf STDERR "ERROR: can not find gc5Base.bw file:\n\t'%s'\n", $gc5Bw; 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 $averageGC = `bigWigInfo $gc5Bw | egrep "mean:" | sed -e 's/mean: //;'`; +my $averageGC = `/cluster/bin/x86_64/bigWigInfo $gc5Bw | egrep "mean:" | sed -e 's/mean: //;'`; chomp $averageGC; $averageGC = sprintf("%.2f", $averageGC); print <<_EOF_ <h2>Description</h2> <p> The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows on the $assemblyDate $em${organism}$noEm/$asmId/$ncbiAssemblyId genome assembly. High GC content is typically associated with gene-rich areas. The average overall GC percent for the entire assembly is % $averageGC. </p> <p> This track may be configured in a variety of ways to highlight different