76aada406b7f8e257b9c6e975138735c3328eff3
galt
  Sat Apr 10 01:52:47 2021 -0700
improving hg38 bigZips downloads for gc5Base

diff --git src/hg/makeDb/doc/hg38/patchUpdate.11.txt src/hg/makeDb/doc/hg38/patchUpdate.11.txt
index 1c36f2e..28285ff 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.11.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.11.txt
@@ -47,43 +47,57 @@
       echo $table
       hgsql hg38 -e "insert into hg38.$table select * from grcH38P11.$table"
     done
 
 
 ##############################################################################
 # Extend main database gc5BaseBw.bw (DONE - 2018-08-06 - Angie)
 
     cd /hive/data/genomes/hg38/bed/gc5Base/
     # Concatenate original assembly results with grcH38P11 results
     time (zcat hg38.gc5Base.wigVarStep.gz \
         /hive/data/genomes/grcH38P11/bed/gc5Base/grcH38P11.gc5Base.wigVarStep.gz \
       | gzip -c \
       > hg38.p11.gc5Base.wigVarStep.gz)
 #real    8m10.061s
+
     # Make a new gc5BaseBw.bw
     time wigToBigWig hg38.p11.gc5Base.wigVarStep.gz ../../chrom.sizes.p11 \
       hg38.p11.gc5Base.bw
 #real    16m28.272s
 
     # Install
     cd /hive/data/genomes/hg38/bed/gc5Base/
     # For the first update only, move initial release files to .initial.  Don't do this next update!
     mv hg38.gc5Base.wigVarStep.gz hg38.initial.gc5Base.wigVarStep.gz
-    ln -s hg38.p11.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
     mv hg38.gc5Base.bw hg38.initial.gc5Base.bw
+    # End of first-update-only stuff
+    
+    ln -s hg38.p11.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
     ln -s hg38.p11.gc5Base.bw hg38.gc5Base.bw
 
+    # Because of this symlink, browser track gc5BaseBw has been automatically updated:
+    # /gbdb/hg38/bbi/gc5BaseBw/gc5Base.bw -> /cluster/data/hg38/bed/gc5Base/hg38.gc5Base.bw
+
+    # For the first update only.  Don't do this next update!
+    # The .wib and .wig.gz are obsolete, remove them from the downloads.
+    rm /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/hg38.gc5Base.wib
+    rm /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/hg38.gc5Base.wig.gz
+    # link the bigwig to downloads
+    ln -sf /hive/data/genomes/hg38/bed/gc5Base/hg38.gc5Base.bw /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/hg38.gc5Base.bw
+    # End of first-update-only stuff
+
 
 ##############################################################################
 # Extend main database download files (DONE - 2018-08-06 - Angie)
     cd /hive/data/genomes/hg38/goldenPath/bigZips
     mkdir p11
     # hg38.2bit was already extended above.
     ln -sf /hive/data/genomes/hg38/hg38.p11.2bit p11/
 
     # AGP:
     zcat hg38.agp.gz \
          /hive/data/genomes/grcH38P11/goldenPath/bigZips/grcH38P11.agp.gz \
     | grep -v ^# \
     | gzip -c > p11/hg38.p11.agp.gz
 
     # FASTA