306ac860b33fbb420c46eeab993b6adb740cc65b
hiram
  Tue Jun 24 10:16:59 2025 -0700
Eliminate gfidx indexes from downloads

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 0502561319d..5c5c233888b 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -131,30 +131,31 @@
   `rm -f "${gbdbDir}/${accessionId}.chrom.sizes.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.bb"`;
   `rm -f "${gbdbDir}/${accessionId}.chromAlias.bb"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
   `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 "${gbdbDir}/${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 "${destDir}/groups.txt"`;
@@ -195,38 +196,38 @@
      `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${gbdbDir}/${accessionId}.2bit"`;
    }
    if (-s "${buildDir}/${asmId}.fa.gz") {
       `ln -s "${buildDir}/${asmId}.fa.gz" "${destDir}/${accessionId}.fa.gz"`;
    } else {
       printf STDERR "# error missing ${asmId}.fa.gz\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.fa.gz" "${destDir}/${accessionId}.chrNames.fa.gz"` if (-s "${buildDir}/${asmId}.chrNames.fa.gz");
    if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt") {
       `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${destDir}/${accessionId}.2bit.bpt"`;
       `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${gbdbDir}/${accessionId}.2bit.bpt"`;
    } else {
       printf STDERR "# error missing ${asmId}.masked.2bit.bpt\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.2bit" "${destDir}/${accessionId}.chrNames.2bit"` if (-s "${buildDir}/${asmId}.chrNames.2bit");
-   if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
-      if (-s "${buildDir}/${accessionId}.trans.gfidx") {
-        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
-        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
-        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${dynaDir}/${accessionId}.untrans.gfidx"`;
-        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${dynaDir}/${accessionId}.trans.gfidx"`;
-      }
-   }
+#   if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
+#      if (-s "${buildDir}/${accessionId}.trans.gfidx") {
+#        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
+#        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
+#        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${dynaDir}/${accessionId}.untrans.gfidx"`;
+#        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${dynaDir}/${accessionId}.trans.gfidx"`;
+#      }
+#   }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
    if (-s "${buildDir}/${asmId}.chrom.sizes") {
     `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"`;
     `ln -s "${buildDir}/${asmId}.chrom.sizes" "${gbdbDir}/${accessionId}.chrom.sizes.txt"`;
    }
    if (-s "${buildDir}/${asmId}.chromAlias.txt") {
     `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"`;
    }
    if (-s "${buildDir}/${asmId}.chromAlias.bb") {
      `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${destDir}/${accessionId}.chromAlias.bb"`;
      `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${gbdbDir}/${accessionId}.chromAlias.bb"`;
    }
    `ln -s "${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}/${asmId}.repeatModeler.out.gz");
@@ -247,21 +248,24 @@
        `ln -s "${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}/${asmId}.userTrackDb.txt") {
+    `ln -s "${buildDir}/${asmId}.userTrackDb.txt" "${destDir}/${accessionId}.userTrackDb.txt"`;
+    `ln -s "${buildDir}/${asmId}.userTrackDb.txt" "${gbdbDir}/${accessionId}.userTrackDb.txt"`;
+   }
    if (-s "${buildDir}/${asmId}.bigMaf.trackDb.txt") {
      `rm -f "${destDir}/${asmId}.bigMaf.trackDb.txt"`;
      `ln -s "${buildDir}/${asmId}.bigMaf.trackDb.txt" "${destDir}/${asmId}.bigMaf.trackDb.txt"`;
    }
 }