1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e
markd
  Tue Jul 29 12:15:26 2025 -0700
import of GENCODE Versions V49, V49lift37, and VM38

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index b17c21deae7..c307dae8a84 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -553,30 +553,76 @@
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release
 
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre}
     pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${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 ${ver} ${ensver} "${ensdate}"
 
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
+    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner
+
+    # if final release, Update 'Release Notes' 
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    jkmake DBS=mm39
+
+    pushd
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+
+    jkmake DBS=mm39 alpha
+##############################################################################
+2025-07-29: import of UCSC GENCODE group processing of GENCODE VM38 pre-release for GENCODE Versions (markd)
+
+   # set shell variable:
+   # pre-release shell variables 
+       ver=M38
+       ensver=115
+       pre="Pre"
+       ensdate='July 2025 pre-release' 
+   # release shell variables 
+       ver=M38
+       ensver=115
+       pre=""
+       ensdate='August 2025'
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre}
+    pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/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 ${ver} ${ensver} "${ensdate}"
+
+
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner
 
     # if final release, Update 'Release Notes' 
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     jkmake DBS=mm39
 
     pushd
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
 
     jkmake DBS=mm39 alpha