cdd0101336b3399e8d1a204a298b017a2675cc3a
hiram
  Fri Jan 24 10:35:41 2020 -0800
now correctly using this asmHubs directories as toolsDir to obtain commonName listings refs #24748

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index b9dcb81..27b64ec 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -1,90 +1,90 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use File::Basename;
 
 my $argc = scalar(@ARGV);
 if ($argc != 2) {
   printf STDERR "mkSymLinks Name asmName\n";
   printf STDERR "e.g.: mkAsmStats Mammals mammals\n";
   exit 255;
 }
 my $Name = shift;
 my $asmHubName = shift;
 
 my %betterName;	# key is asmId, value is common name
 my $srcDocDir = "${asmHubName}AsmHub";
 
 my $home = $ENV{'HOME'};
-my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 my $commonNameList = "$asmHubName.asmId.commonName.tsv";
 my $commonNameOrder = "$asmHubName.commonName.asmId.orderList.tsv";
 
-open (FH, "<$srcDir/${commonNameList}") or die "can not read $srcDir/${commonNameList}";
+open (FH, "<$toolsDir/${commonNameList}") or die "can not read $toolsDir/${commonNameList}";
 while (my $line = <FH>) {
   chomp $line;
   my ($asmId, $name) = split('\t', $line);
   $betterName{$asmId} = $name;
 }
 close (FH);
 
 my @orderList;	# asmId of the assemblies in order from the *.list files
 # the order to read the different .list files:
 my $assemblyCount = 0;
 
-open (FH, "<$srcDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
+open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   ++$assemblyCount;
 }
 close (FH);
 
 my $destDir = "/hive/data/genomes/asmHubs";
 
 my $orderKey = 1;
 foreach my $asmId (reverse(@orderList)) {
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
   $accessionDir .= "/" . $asmId;
   $destDir = "/hive/data/genomes/asmHubs/$accessionDir";
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir";
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
   printf STDERR "ln -s '${buildDir}' '${destDir}'\n";
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${asmId}.2bit"`;
   `rm -f "${destDir}/${asmId}.agp.gz"`;
   `rm -f "${destDir}/${asmId}.chrom.sizes"`;
   `rm -f "${destDir}/${asmId}_assembly_report.txt"`;
   `rm -f "${destDir}/${asmId}.trackDb.txt"`;
   `rm -f "${destDir}/${asmId}.genomes.txt"`;
   `rm -f "${destDir}/${asmId}.hub.txt"`;
   `rm -f "${destDir}/${asmId}.groups.txt"`;
   `ln -s "${buildDir}/bbi" "${destDir}/bbi"`;
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`;
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"`;
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
    if ($jpgFiles > 0) {
     `rm -f ${destDir}/html/*.jpg`;
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
   `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/"`;
   `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/"`;
   `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/"`;
 }