7f3a7738bd88d2762069a28e9ee35039fa915f48
markd
  Wed Jan 26 07:28:30 2022 -0800
import of GENCODE V40 pre-release

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index e35b175..ea53c4e 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -936,15 +936,50 @@
     # edit human/hg38/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=hg38
 
     # edit all.joiner to add ~/tmp/gencodeV39.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV39/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
 
 
 #########################################################################
+2022-01-25: import of UCSC GENCODE group processing of GENCODE V40 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/gencodeV40/hgcImportPre
+    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImportPre
+
+    (time nice make -O -j 32 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # reported stray space in
+    release_40/gencode.v40.metadata.Pubmed_id.gz
+
+    # 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 40 106 'Feb 2022'
+
+    # 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/hgcImportPre
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+#########################################################################
+