37b85e32f377f44aca6f57162c38ac49cc70c678
hiram
  Sat Oct 2 00:36:26 2021 -0700
adding rmsk output to downloads and correctly getting assembly_report on downloads refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 78870dc..c09c5ae 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -81,30 +81,31 @@
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.untrans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.trans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.agp.gz"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.txt"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
+  `rm -f "${destDir}/${accessionId}.repeatMasker.out.gz"`;
   `rm -f "${destDir}/${accessionId}.userTrackDb.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/download.genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
   `rm -f "${destDir}/download.hub.txt"`;
   `rm -f "${destDir}/groups.txt"`;
   `ln -s "${buildDir}/bbi" "${destDir}/bbi"` if (-d "${buildDir}/bbi");
   `ln -s "${buildDir}/genes" "${destDir}/genes"` if (-d "${buildDir}/genes");
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
   `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"` if (-d "${buildDir}/liftOver");
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
@@ -113,31 +114,32 @@
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
   `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/${asmId}.2bit");
    if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
       if (-s "${buildDir}/${accessionId}.trans.gfidx") {
         `rm -f "${buildDir}/${asmId}.untrans.gfidx"`;
         `rm -f "${buildDir}/${asmId}.trans.gfidx"`;
         `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
         `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
       }
    }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"` if (-s "${buildDir}/${asmId}.chrom.sizes");
   `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"` if (-s "${buildDir}/${asmId}.chromAlias.txt");
-  `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/${asmId}_assembly_report.txt");
+  `ln -s "${buildDir}/${asmId}.repeatMasker.out.gz" "${destDir}/${accessionId}.repeatMasker.out.gz"` if (-s "${buildDir}/${asmId}.repeatMasker.out.gz");
+  `ln -s "${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");
    if (-s "${buildDir}/${asmId}.singleFile.hub.txt") {
     `ln -s "${buildDir}/${asmId}.singleFile.hub.txt" "${destDir}/hub.txt"`;
     `ln -s "${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}/${asmId}.hub.txt");
    }
   `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/groups.txt"` if (-s "${buildDir}/${asmId}.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"`;