516ff15a73f51f29466f148d163ec3d83d9e41fb
markd
  Thu Jan 16 13:45:55 2020 -0800
import of GENCODE V33

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 71cade7..953cbfa 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -551,47 +551,80 @@
     Changes:
     wgEncodeGencode2wayConsPseudoV32.gp 
     wgEncodeGencodeAttrsV32.tab
     wgEncodeGencodePolyaV32.gp
     wgEncodeGencodeTagV32.tab
     only attrs and maybe tags matter to hgGene gencode
 
     mkdir pre-diffs
     diff ../gencodeV32pre/tables/wgEncodeGencodeAttrsV32.tab tables/wgEncodeGencodeAttrsV32.tab >pre-diffs/wgEncodeGencodeAttrsV32.diff
     diff ../gencodeV32pre/tables/wgEncodeGencodeTagV32.tab tables/wgEncodeGencodeTagV32.tab >pre-diffs/wgEncodeGencodeTagV32.diff
 
     # wgEncodeGencodeAttrsV32: experimental conformation level changed on a few pseudogenes
     # wgEncodeGencodeTagV32: pseudo_consens changed on a few pseudogenes.
 
 #########################################################################
-2019-11-15: import of UCSC GENCODE group processing of GENCODE V32 (markd)
-    # PRE-RELEASE
+2019-11-15: import of UCSC GENCODE group processing of GENCODE V33 PRE-RELEASE (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
 
     # download, build and load tables
     mkdir -p /hive/data/genomes/hg38/bed/gencodeV33
     pushd /hive/data/genomes/hg38/bed/gencodeV33
 
     (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
 
     # compare tables from previous release to see if number changed makes
     # sense.  Results are in gencode-cmp.tsv
 
     # generate trackDb and joiner blurb
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg38 33 99 'Nov 2019'
 
     # If being pushed public, update 'Release Notes' in
     # human/hg38/wgEncodeGencodeSuper.html
 
     # edit human/hg38/trackDb.gencode.ra to add new .ra file include
     make DBS=hg38
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeV33.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV33
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # commit all
 
 #########################################################################
+2020-01-16: import of UCSC GENCODE group processing of GENCODE V33  (markd)
+    # deprecate pre-release
+    mv /hive/data/genomes/hg38/bed/gencodeV33 /hive/data/genomes/hg38/bed/gencodeV33pre
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg38/bed/gencodeV33
+    pushd /hive/data/genomes/hg38/bed/gencodeV33
+
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg38 33 99 'Jan 2020'
+
+    # If being pushed public, update 'Release Notes' in
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    make DBS=hg38
+
+    ## only if being pushed to RR (may be there from pre-release)
+    # edit all.joiner to add ~/tmp/gencodeV33.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV33
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+
+#########################################################################