8dbae0dc03900f90cf27c96aefb8996591edc7e1
hiram
  Mon May 12 12:39:19 2025 -0700
construction symLinks for contrib tracks refs #34917

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index fe066ad8c65..0502561319d 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -14,30 +14,32 @@
   printf STDERR "the result will create symLinks from the build direcory\n";
   printf STDERR "into the appropriate /asmHubs/GC[AF]/.../ release directory\n";
   printf STDERR "hierarchy.  The output to stderr is merely a progress report.\n";
   exit 255;
 }
 
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 my $inputList = shift;
 my $orderList = $inputList;
 if ( ! -s "$orderList" ) {
   $orderList = $toolsDir/$inputList;
 }
 
+my @stageHub = qw( alpha beta public );
+
 my %commonName;	# key is asmId, value is common name
 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, "<${orderList}") or die "can not read ${orderList}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($asmId, $commonName) = split('\t', $line);
   if (defined($commonName{$asmId})) {
     printf STDERR "ERROR: duplicate asmId: '%s'\n", $asmId;
     printf STDERR "previous name: '%s'\n", $commonName{$asmId};
     printf STDERR "duplicate name: '%s'\n", $commonName;
     exit 255;
@@ -87,30 +89,32 @@
   ++$buildDone;
   printf STDERR "# %03d symlinks %s %s\n", $buildDone, $asmId, $commonName{$asmId};
 #  printf STDERR "%s\n", $buildDir;
 #  printf STDERR "%s\n", $destDir;
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
   if ( ! -d "${dynaDir}" ) {
     `mkdir -p "${dynaDir}"`;
   }
   if ( ! -d "${gbdbDir}" ) {
     `mkdir -p "${gbdbDir}"`;
   }
   `rm -f "${destDir}/bbi"`;
   `rm -fr "${gbdbDir}/bbi"`;
+  `rm -f "${destDir}/contrib"`;
+  `rm -f "${gbdbDir}/contrib"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
   `rm -f "${gbdbDir}/liftOver"`;
   `rm -f "${destDir}/otherAligners"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -fr "${gbdbDir}/html"`;
   `rm -fr "${gbdbDir}/ixIxx"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
   `rm -f "${dynaDir}/${accessionId}.2bit"`;
   `rm -f "${gbdbDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.chrNames.2bit"`;
   `rm -f "${destDir}/${accessionId}.fa.gz"`;
@@ -132,41 +136,49 @@
   `rm -f "${destDir}/${accessionId}.rmsk.customLib.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatMasker.out.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatMasker.version.txt"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.version.txt"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.families.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.families.stk.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.out.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.2bit"`;
   `rm -f "${destDir}/${accessionId}.rmod.log.txt"`;
   `rm -f "${destDir}/${accessionId}.userTrackDb.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/download.genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
   `rm -f "${gbdbDir}/hub.txt"`;
+  foreach my $hubTxt (@stageHub) {
+    `rm -f "${destDir}/$hubTxt.hub.txt"`;
+    `rm -f "${gbdbDir}/$hubTxt.hub.txt"`;
+  }
   # it used to be standard practice to have a different hub.txt on genome-test
   #   vs. the hub.txt on hgdownload.  They evolved into being identical, but
   #   there may be a case in the future where this function may be required.
   #   Also, the sendDownload script expects to use this download.hub.txt file.
   `rm -f "${destDir}/download.hub.txt"`;
   `rm -f "${destDir}/groups.txt"`;
   `rm -f "${gbdbDir}/groups.txt"`;
    if (-d "${buildDir}/bbi") {
      `ln -s "${buildDir}/bbi" "${destDir}/bbi"`;
      `ln -s "${buildDir}/bbi" "${gbdbDir}/bbi"`
    }
+   if (-d "${buildDir}/contrib") {
+    `ln -s "${buildDir}/contrib" "${destDir}/contrib"`;
+    `ln -s "${buildDir}/contrib" "${gbdbDir}/contrib"`;
+   }
   `ln -s "${buildDir}/genes" "${destDir}/genes"` if (-d "${buildDir}/genes");
    if (-d "${buildDir}/ixIxx") {
      `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`;
      `ln -s "${buildDir}/ixIxx" "${gbdbDir}/ixIxx"`;
    }
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
    if (-d "${buildDir}/liftOver") {
       `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"`;
       `ln -s "${buildDir}/liftOver" "${gbdbDir}/liftOver"`;
    }
   `ln -s "${buildDir}/otherAligners" "${destDir}/otherAligners"` if (-d "${buildDir}/otherAligners");
    if (-d "${buildDir}/html") {
      `ln -s ${buildDir}/html/*.html "${destDir}/html/"`;
      `ln -s ${destDir}/html "${gbdbDir}/html"`;
    }
@@ -218,30 +230,36 @@
    `ln -s "${buildDir}/${asmId}.rmsk.customLib.fa.gz" "${destDir}/${accessionId}.rmsk.customLib.fa.gz"` if (-s "${buildDir}/${asmId}.rmsk.customLib.fa.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.out.gz" "${destDir}/${accessionId}.repeatMasker.out.gz"` if (-s "${buildDir}/${asmId}.repeatMasker.out.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.out.gz" "${destDir}/${accessionId}.repeatModeler.out.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.out.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.version.txt" "${destDir}/${accessionId}.repeatMasker.version.txt"` if (-s "${buildDir}/${asmId}.repeatMasker.version.txt");
   `ln -s "${buildDir}/${asmId}.repeatModeler.version.txt" "${destDir}/${accessionId}.repeatModeler.version.txt"` if (-s "${buildDir}/${asmId}.repeatModeler.version.txt");
   `ln -s "${buildDir}/${asmId}.repeatModeler.families.fa.gz" "${destDir}/${accessionId}.repeatModeler.families.fa.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.families.fa.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.families.stk.gz" "${destDir}/${accessionId}.repeatModeler.families.stk.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.families.stk.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.2bit" "${destDir}/${accessionId}.repeatModeler.2bit"` if (-s "${buildDir}/${asmId}.repeatModeler.2bit");
   `ln -s "${buildDir}/${asmId}.rmod.log.txt" "${destDir}/${accessionId}.rmod.log.txt"` if (-s "${buildDir}/${asmId}.rmod.log.txt");
   `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/download/${asmId}_assembly_report.txt");
   # trackDb.txt still needed for use by top-level genomes.txt file
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/trackDb.txt"` if (-s "${buildDir}/${asmId}.trackDb.txt");
   # genomes.txt obsolete now with single file
 #   `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/genomes.txt"` if (-s "${buildDir}/${asmId}.genomes.txt");
   `ln -s "${buildDir}/${asmId}.download.genomes.txt" "${destDir}/download.genomes.txt"` if (-s "${buildDir}/${asmId}.download.genomes.txt");
+   foreach my $hubTxt (@stageHub) {
+     if (-s "${buildDir}/${hubTxt}.hub.txt") {
+       `ln -s "${buildDir}/${hubTxt}.hub.txt" "${destDir}/${hubTxt}.hub.txt"`;
+       `ln -s "${buildDir}/${hubTxt}.hub.txt" "${gbdbDir}/${hubTxt}.hub.txt"`;
+     }
+   }
    if (-s "${buildDir}/${asmId}.singleFile.hub.txt") {
     `ln -s "${buildDir}/${asmId}.singleFile.hub.txt" "${destDir}/hub.txt"`;
     `ln -s "${buildDir}/${asmId}.singleFile.hub.txt" "${gbdbDir}/hub.txt"`;
     `ln -s "${buildDir}/${asmId}.download.hub.txt" "${destDir}/download.hub.txt"` if (-s "${buildDir}/${asmId}.download.hub.txt");
    } else {
     `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/hub.txt"` if (-s "${buildDir}/${asmId}.hub.txt");
    }
    if (-s "${buildDir}/${asmId}.groups.txt") {
       `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/groups.txt"`;
       `ln -s "${buildDir}/${asmId}.groups.txt" "${gbdbDir}/groups.txt"`;
    }
   `ln -s "${buildDir}/${asmId}.userTrackDb.txt" "${destDir}/${accessionId}.userTrackDb.txt"` if ( -s "${buildDir}/${asmId}.userTrackDb.txt");
    if (-s "${buildDir}/${asmId}.bigMaf.trackDb.txt") {
      `rm -f "${destDir}/${asmId}.bigMaf.trackDb.txt"`;
      `ln -s "${buildDir}/${asmId}.bigMaf.trackDb.txt" "${destDir}/${asmId}.bigMaf.trackDb.txt"`;