8debce5b56bcc570ddff4226bf9b04c30e4f6f29
markd
  Wed Feb 5 12:48:04 2025 -0800
import of GENCODE Versions VM37, V48, V48lift37

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index cfa5790fa36..6d102c7ebba 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -1360,15 +1360,58 @@
     # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner
 
     # if final release, Update 'Release Notes' 
     #  human/hg19/wgEncodeGencodeSuper.html
 
     jkmake DBS=hg19
 
     # check joiner 
     pushd /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg19 alpha
 #########################################################################
+2025-02-05: import of UCSC GENCODE group processing of GENCODE V48lift38 pre-release for GENCODE Versions (markd)
+   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release type and versions
+
+   # pre-release shell variables 
+       ver=48lift37
+       ensver=114
+       pre="Pre"
+       ensdate='Feb 2025 pre-release' 
+   # release shell variables 
+       ver=48lift37
+       ensver=114
+       pre=""
+       ensdate='Mar 2025' 
+    
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}
+    pushd /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}
+
+    (time nice make -O -j 32 -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
+    ../outside/gencode/bin/gencodeGenerateTrackDbs hg19 ${ver} ${ensver} "${ensdate}"
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner
+
+    # if final release, Update 'Release Notes' 
+    #  human/hg19/wgEncodeGencodeSuper.html
+
+    jkmake DBS=hg19
+
+    # check joiner 
+    pushd /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg19 alpha
+#########################################################################