16e9b95f19b004854554c583f341e16d496a7253
angie
  Wed Apr 10 10:21:06 2019 -0700
Changing bigZips/latest from just a link to the most recent dir (p12) to a dir with versionless files, to make it easier for pipelines.  refs #23198

diff --git src/hg/makeDb/doc/hg38/patchUpdate.12.txt src/hg/makeDb/doc/hg38/patchUpdate.12.txt
index 05569b4..04554f8 100644
--- src/hg/makeDb/doc/hg38/patchUpdate.12.txt
+++ src/hg/makeDb/doc/hg38/patchUpdate.12.txt
@@ -55,31 +55,32 @@
       | 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 - 2018-11-11 - Angie)
+# Extend main database download files (DONE - 2019-04-10 - Angie)
+# Previously done 2018-11-11
 
     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
@@ -128,37 +129,47 @@
 
     # RepeatMasker .align files:
     zcat hg38.fa.align.gz /hive/data/genomes/grcH38P12/bed/repeatMasker/grcH38P12.fa.align.gz \
     | gzip -c > p12/hg38.p12.fa.align.gz
 
     # Make new md5sum.txt
     cd p12
     md5sum hg38.* > md5sum.txt
 
     # Install
     # 11/1/18 -- leave bigZips/ top-level files unchanged (links to initial not p12)
     cd /hive/data/genomes/hg38/goldenPath/bigZips
     for file in initial/*; do
       ln -sf $file .
     done
-    rm -f latest
-    ln -s p12 latest
+    # 4/10/19: make latest a real dir with versionless filenames.
+    rm -rf latest
+    mkdir latest
+    cd latest
+    for file in ../p12/*; do
+      noVersion=$(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 p12 \
+    ln -s /hive/data/genomes/hg38/goldenPath/bigZips/latest \
       /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/latest
 
 
 #########################################################################
 # 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