07942970a19230fee2cbb6bf8ae1c15427533c66
markd
  Wed Jan 26 08:53:49 2022 -0800
loaded GENCODE VM29 pre-release

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 9c34410..575679a 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -139,15 +139,48 @@
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # add ticket and MARK QA READY
 
 ##############################################################################
+2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 pre-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/gencodeVM29/hgcImportPre
+    pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
+
+    (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 M29 106 'Feb 2022'
+
+    # Update 'Release Notes' in
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    # edit human/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/gencodeVM29/hgcImportPre.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=mm39 alpha
+    # if pushing public: add ticket and MARK QA READY
+
+##############################################################################