f1a6509a2f33b00f4908de15d47f6625118b6a93
markd
  Thu Nov 3 12:46:19 2022 -0700
import of All GENCODE VM31

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index ff05e43..5d42764 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -259,15 +259,49 @@
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM30/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
+2022-11-03: import of UCSC GENCODE group processing of GENCODE VM31 release (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport
+    pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport
+
+    # get initial version of transcript_rankings,
+    http://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_mouse/release_M31/gencode.vM31.transcript_rankings.txt.gz
+
+    (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
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M31 108 'Oct 2022'
+
+    # Update 'Release Notes' in
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=mm39
+
+    ## only if being pushed to RR:
+    # edit all.joiner to add ~/tmp/gencodeVM31/hgcImport.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=mm39 alpha
+##############################################################################