ba39846fb30a64ba6df41c0aae781915ddf61c80
markd
  Mon Mar 4 22:15:06 2024 -0800
import of GENCODE VM35

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 02a5955..5a316ca 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -440,15 +440,52 @@
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     jkmake DBS=mm39
 
     # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner
     # already added for pre-release
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
+2024-03-04: import of UCSC GENCODE group processing of GENCODE VM35 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/gencodeVM35/hgcImport${pre}
+    pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${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 'April 2024'
+
+    # 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/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
+##############################################################################