24d69a7106a0e67837d07d860924733c30ba66e2
markd
  Fri May 13 12:48:37 2022 -0700
import of gencode V41 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 8c8c1f4..e805e62 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -1012,16 +1012,46 @@
     # 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/gencodeV40.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
 #########################################################################
+2022-05-13: import of UCSC GENCODE group processing of GENCODE V41 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/gencodeV41/hgcImportPre
+    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImportPre
+
+    (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 41 107 'June 2022'
 
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include, as alpha
+
+    # edit all.joiner to add ~/tmp/gencodeV41.joiner
+
+    jkmake DBS=hg38
+
+    # check joiner 
+    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImportPre
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+
+#########################################################################