584d70ac259b9b2f818e40a2f838ac114e4b234d
markd
  Tue Apr 25 19:58:18 2023 -0700
import of gencode V44 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 7ab84d8..c59fc5f 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -1182,15 +1182,50 @@
     # Update 'Release Notes' (for final)
     # human/hg38/wgEncodeGencodeSuper.html
 
     # edit human/hg38/trackDb.gencode.ra to remove alpha
     jkmake DBS=hg38
 
     # check joiner 
     pushd /hive/data/genomes/hg38/bed/gencodeV43/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
 
 #########################################################################
+2023-04-25: import of UCSC GENCODE group processing of GENCODE V44 pre-release for hgc all gencode  (markd)
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    pre="Pre"
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg38/bed/gencodeV44/hgcImport${pre}
+    pushd /hive/data/genomes/hg38/bed/gencodeV44/hgcImport${pre}
+
+    (time nice make -O -j 32 -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/gencodeGenerateTrackDbs hg38 44 110 'May 2023'
+
+    # edit all.joiner to add ~/tmp/gencodeV44.joiner
+
+    # Update 'Release Notes' (for final, not pre)
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to remove alpha
+    jkmake DBS=hg38
+
+    # check joiner 
+    pushd /hive/data/genomes/hg38/bed/gencodeV44/hgcImport${pre}
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+
+#########################################################################