308bed30e11953a0dc802743c98181ce7f409dd9
markd
  Tue Oct 10 20:23:18 2023 -0700
import of pre-release of GENCODE V45, VM34, and V45lift37

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 08f1e74..bb1d192 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -367,15 +367,51 @@
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit all.joiner to add ~/tmp/gencodeVM33/hgcImport${pre}.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre}
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
+2023-04-25: import of UCSC GENCODE group processing of GENCODE VM34 pre-release (markd)
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # set shell variable:
+    pre="Pre"
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
+    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
+
+    (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 M34 111 'Nov 2023'
+
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
+
+    ## only if being pushed to RR:
+    # Update 'Release Notes' in
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    jkmake DBS=mm39
+
+    # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=mm39 alpha
+##############################################################################