44e8a323a9251919f1dada93f0d389a555fda1a2
markd
  Tue Apr 6 23:14:27 2021 -0700
Import gencode V38 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 3d7cad7..d618dc8 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -826,15 +826,47 @@
 
     # edit human/hg38/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=hg38
 
     ## only if being pushed to RR (may be there from pre-release)
     # edit all.joiner to add ~/tmp/gencodeV37.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV37/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
     # if pushing public: create ticket and MARK QA READY
 #########################################################################
+2021-04-06: (PRE-RELEASE) import of UCSC GENCODE group processing of GENCODE V38 for hgc all gencode  (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/gencodeV38Pre/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV38Pre/hgcImport
+
+    (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
+    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 38 104 'Apr 2021'
+
+    # Update 'Release Notes' (for final)
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=hg38
+
+    # edit all.joiner to add ~/tmp/gencodeV38.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV38Pre/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+    # if pushing public: create ticket and MARK QA READY
+#########################################################################