b80a59e82af6a5a67934e199bf4113950f9c4706
angie
  Wed Jul 24 15:58:57 2019 -0700
Updating hgdownload-test link for hg38/bigZips/hg38.chrom.sizes and adding hg38*.chrom.sizes links to subdirectories.

diff --git src/hg/makeDb/doc/hg38/patchUpdate.12.txt src/hg/makeDb/doc/hg38/patchUpdate.12.txt
index 04554f8..f26cac2 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.12.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.12.txt
@@ -55,33 +55,35 @@
       | gzip -c \
       > hg38.p12.gc5Base.wigVarStep.gz)
 #real    8m9.913s
     # Make a new gc5BaseBw.bw
     time wigToBigWig hg38.p12.gc5Base.wigVarStep.gz ../../chrom.sizes.p12 \
       hg38.p12.gc5Base.bw
 #real    16m33.792s
 
     # Install
     cd /hive/data/genomes/hg38/bed/gc5Base/
     ln -sf hg38.p12.gc5Base.wigVarStep.gz hg38.gc5Base.wigVarStep.gz
     ln -sf hg38.p12.gc5Base.bw hg38.gc5Base.bw
 
 
 ##############################################################################
-# Extend main database download files (DONE - 2019-04-10 - Angie)
+# Extend main database download files (DONE - 2019-07-24 - Angie)
 # Previously done 2018-11-11
 
+# NOTE FOR NEXT TIME: set up hg38*.chrom.sizes links correctly the first time (see 7/24/19)
+
     cd /hive/data/genomes/hg38/goldenPath/bigZips
     mkdir p12
     # hg38.2bit was already extended above.
     ln -sf /hive/data/genomes/hg38/hg38.p12.2bit p12/
 
     # AGP:
     zcat hg38.agp.gz \
          /hive/data/genomes/grcH38P12/goldenPath/bigZips/grcH38P12.agp.gz \
     | grep -v ^# \
     | gzip -c > p12/hg38.p12.agp.gz
 
     # FASTA
     twoBitToFa ../../hg38.p12.2bit stdout \
     | gzip -c > p12/hg38.p12.fa.gz
     faSize p12/hg38.p12.fa.gz
@@ -148,30 +150,40 @@
     for file in ../p12/*; do
       noVersion=$(echo $(basename $file) | sed -e 's/.p12//')
       ln -s $file $noVersion
     done
     rm md5sum.txt
     md5sum hg38* > md5sum.txt
     echo GRCh38.p12 > LATEST_VERSION
 
     rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p12
     ln -s /hive/data/genomes/hg38/goldenPath/bigZips/p12 \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p12
     rm -f /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
     ln -s /hive/data/genomes/hg38/goldenPath/bigZips/latest \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
 
+    # 7/24/19: make correct links for chrom.sizes
+    ln -sf /hive/data/genomes/hg38/chrom.sizes.initial \
+      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/hg38.chrom.sizes
+    ln -sf /hive/data/genomes/hg38/chrom.sizes.initial \
+      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/initial/hg38.chrom.sizes
+    ln -sf /hive/data/genomes/hg38/chrom.sizes \
+      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest/hg38.chrom.sizes
+    ln -sf /hive/data/genomes/hg38/chrom.sizes.p12 \
+      /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/p12/hg38.p12.chrom.sizes
+
 
 #########################################################################
 # Regenerate idKeys with extended hg38 (DONE - 2018-08-10 - Angie)
 
     mkdir /hive/data/genomes/hg38/bed/idKeys.p12
     cd /hive/data/genomes/hg38/bed/idKeys.p12
     # ku down... use hgwdev this time:
     time ($HOME/kent/src/hg/utils/automation/doIdKeys.pl \
       -twoBit=/hive/data/genomes/hg38/hg38.p12.unmasked.2bit \
       -bigClusterHub=hgwdev -smallClusterHub=hgwdev \
         -buildDir=`pwd` hg38) > do.log 2>&1 &
     tail -f do.log
 #real    1m21.903s
     cat hg38.keySignature.txt
 #c9c5d621a52f96886fa9cd785c99248f