d19ef54d64fd2e113d0636b1633214ddfb837856
markd
  Thu Jan 11 17:54:48 2024 -0800
GENCODE VM34 import

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index bb1d192..02a5955 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -403,15 +403,52 @@
     ## 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
 ##############################################################################
+2024-01-11: import of UCSC GENCODE group processing of GENCODE VM34 final elease (markd)
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # set shell variable:
+    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 'Jan 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/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
+##############################################################################