ea88d6b1ce6aaff5f1e3574f9607de1276b929c9
galt
  Sun Apr 11 11:15:22 2021 -0700
Revert "hg19 gc5Base makedoc tweak for consistency."

This reverts commit 6bb4a70d43ca7391a27cebc24726be25d639d500.

diff --git src/hg/makeDb/doc/hg19.patchUpdate.13.txt src/hg/makeDb/doc/hg19.patchUpdate.13.txt
index d2e0945..5ba0d38 100644
--- src/hg/makeDb/doc/hg19.patchUpdate.13.txt
+++ src/hg/makeDb/doc/hg19.patchUpdate.13.txt
@@ -58,60 +58,48 @@
 
 
 ##############################################################################
 # Extend main database gc5BaseBw.bw (DONE - 2018-09-28 - Angie)
 # first done 2018-09-17
 # UNDONE 2018-09-28 (see ROLL IT ALL BACK belaow)
 # REDONE (except for first-update-only mv, using initial files) 2018-09-28
 
     cd /hive/data/genomes/hg19/bed/gc5Base/
     # Concatenate original assembly results with grcH37P13 results
     time (zcat hg19.gc5Base.txt.gz \
         /hive/data/genomes/grcH37P13/bed/gc5Base/grcH37P13.gc5Base.wigVarStep.gz \
       | gzip -c \
       > hg19.p13.gc5Base.wigVarStep.gz)
 #real    5m48.392s
-
     # Make a new gc5BaseBw.bw
     time wigToBigWig hg19.p13.gc5Base.wigVarStep.gz ../../chrom.sizes.p13 \
       hg19.p13.gc5Base.bw
 #real    10m57.806s
 
     # Install
     cd /hive/data/genomes/hg19/bed/gc5Base/
     # For the first update only, move initial release files to .initial.  Don't do this next update!
     mv hg19.gc5Base.txt.gz hg19.initial.gc5Base.wigVarStep.gz
     mv gc5Base.bw hg19.initial.gc5Base.bw
     # End of first-update-only stuff
 
     ln -sf hg19.p13.gc5Base.wigVarStep.gz hg19.gc5Base.wigVarStep.gz
     ln -sf hg19.p13.gc5Base.bw hg19.gc5Base.bw
 
     ln -sf /hive/data/genomes/hg19/bed/gc5Base/hg19.gc5Base.wigVarStep.gz \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/gc5Base/hg19.gc5Base.txt.gz
 
-    # Because of this symlink, browser track gc5BaseBw has been automatically updated:
-    # /gbdb/hg19/bbi/gc5Base.bw -> /hive/data/genomes/hg19/bed/gc5Base/hg19.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/hg19/bigZips/hg19.gc5Base.wib
-    rm /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/hg19.gc5Base.wig.gz
-    # link the bigwig to downloads
-    ln -sf /hive/data/genomes/hg19/bed/gc5Base/hg19.gc5Base.bw /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/hg19.gc5Base.bw
-    # End of first-update-only stuff
-
 
 
 ##############################################################################
 # Extend main database download files (DONE - 2019-01-12 - Angie)
 # first done 2018-09-18
 # UNDONE 2018-09-28 (see ROLL IT ALL BACK below)
 # REDONE (except for first-update-only mv) 2018-09-?
 
     cd /hive/data/genomes/hg19/goldenPath/bigZips
     mkdir p13
     # hg19.2bit and chrom.sizes were already extended above.
     ln -sf /hive/data/genomes/hg19/hg19.p13.2bit p13/
     ln -sf /hive/data/genomes/hg19/chrom.sizes.p13 p13/hg19.p13.chrom.sizes
 
     # AGP: