0f6f8c5cdfc1c5385c814102a4fa59afb08d2849
markd
  Wed Jul 31 23:45:27 2024 -0700
import of GENCODE v47, v47lift37, and vM36 pre-releases

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 4b9c97a..d06aa2f 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -477,52 +477,60 @@
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     jkmake DBS=mm39
 
     # edit all.joiner to add ~/tmp/gencodeVM35/hgcImport${pre}.joiner
     # already added for pre-release
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre}
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
-2024-05-14: import of UCSC GENCODE group processing of GENCODE VM35 release (markd)
+2024-07-31: import of UCSC GENCODE group processing of GENCODE VM36 pre-release for GENCODE Versions (markd)
 
-    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
    # set shell variable:
+   # pre-release shell variables 
+       ver=M36
+       ensver=113
+       pre="Pre"
+       ensdate='Sept 2024 pre-release' 
+   # release shell variables 
+       ver=M36
+       ensver=113
        pre=""
+       ensdate='Sept 2024' 
+
+    # 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/gencodeVM35/hgcImport${pre}
-    pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre}
+    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 M35 112 'May 2024'
+    ../../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
 
-    ## only if being pushed to RR:
-    # Update 'Release Notes' in
+    # if final release, Update 'Release Notes' 
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     jkmake DBS=mm39
 
-    # edit all.joiner to add ~/tmp/gencodeVM35/hgcImport${pre}.joiner
-    # already added for pre-release
-    # verify with:
-    pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre}
+    pushd /hive/data/genomes/mm39/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=mm39 alpha
 ##############################################################################