8c68b963e315759727569797b7b32f2bc009a619
angie
  Tue Feb 11 11:25:10 2020 -0800
oops, forgot download files for rebuilt hg38 Self Chain.  refs #24695

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 6e35cae..425d388 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -6848,26 +6848,36 @@
     find /hive/data/genomes/hg38/bed/lastzSelf.2020-01-27/axtChain/run/chain -name "*.chain" \
     | chainMergeSort -inputList=stdin \
     | nice gzip -c \
       > /hive/data/genomes/hg38/bed/lastzSelf.2020-01-27/axtChain/hg38.hg38.all.chain.gz
 
     # NOTE FOR NEXT TIME: this filtering step will be unnecessary when -minScore=10000 is used
     # from the beginning.
     # Filter to minScore of 10000 (too much fluff with -minScore=3000) per Jim (see #24695)
     cd /hive/data/genomes/hg38/bed/lastzSelf.2020-01-27/axtChain
     mv hg38.hg38.all.chain.gz hg38.hg38.all.unfiltered.chain.gz
     chainFilter hg38.hg38.all.unfiltered chain.gz -minScore=10000 \
     | gzip -c > hg38.hg38.all.chain.gz
     hgLoadChain -normScore -tIndex hg38 chainSelfRedo hg38.hg38.all.chain.gz
     checkTableCoords hg38 chainSelfRedo
 
-    # Rename to chainSelf and update lastz symlinks
+    # Rename to chainSelf and update lastz symlinks and downloads
     hgsql hg38 -e 'drop table chainSelf; drop table chainSelfLink;
                    rename table chainSelfRedo to chainSelf;
                    rename table chainSelfRedoLink to chainSelfLink;'
     cd /hive/data/genomes/hg38/bed
     rm lastz.self lastz.hg38
     ln -s lastzSelf.2020-01-27 lastz.self
     ln -s lastzSelf.2020-01-27 lastz.hg38
+    cd /hive/data/genomes/hg38/bed/lastzSelf.2020-01-27/axtChain
+    cp /hive/data/genomes/hg38/bed/lastzSelf.2014-01-25/axtChain/README.txt .
+    $EDITOR README.txt
+    md5sum hg38.hg38.all.chain.gz > md5sum.txt
+    # Make sure that the old download dir has only symlinks, no real files, then remove and rebuild.
+    ls -lR /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/vsSelf/
+    rm -r /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/vsSelf/
+    mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/vsSelf/
+    cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/vsSelf/
+    ln -s /hive/data/genomes/hg38/bed/lastzSelf.2020-01-27/axtChain/{README.txt,hg38.hg38.all.chain.gz,md5sum.txt} .
 
 
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