fa5d9035c64f21008b496bc74780a9d0fcc3f2c3
markd
  Thu Dec 29 15:26:11 2022 -0800
import of GENCODE V43 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 5d42d40..0776d67 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -1145,15 +1145,44 @@
     # edit human/hg38/trackDb.gencode.ra to remove alpha
 
     # edit all.joiner to add ~/tmp/gencodeV42.joiner
 
     jkmake DBS=hg38
 
     # check joiner 
     pushd /hive/data/genomes/hg38/bed/gencodeV42/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
 
 #########################################################################
+2022-12-27: import of UCSC GENCODE group processing of GENCODE V43 pre-release 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/gencodeV43/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV43/hgcImport
+
+    (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 43 109 'Jan 2023'
+
+    # edit all.joiner to add ~/tmp/gencodeV43.joiner
+
+    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
+
+#########################################################################