75c0e5568aaddeb999f1ff3e0ad43815025979f9
markd
  Thu Jan 16 15:01:34 2020 -0800
import of GENCODE VM24

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 8c185fb..a3dc3bf 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18264,33 +18264,31 @@
 Longest finished job:            1966s      32.77m     0.55h    0.02d
 Submission to last job:         15067s     251.12m     4.19h    0.17d
 
 # offTargets:
 Completed: 147394 of 147394 jobs
 CPU time in finished jobs:    2213680s   36894.66m   614.91h   25.62d  0.070 y
 IO & Wait Time:               2663355s   44389.25m   739.82h   30.83d  0.084 y
 Average job time:                  33s       0.55m     0.01h    0.00d
 Longest finished job:              68s       1.13m     0.02h    0.00d
 
 #########################################################################
 
 # For ENCODE 3 tracks, see doc/encode3/mouse.txt
 
 ##############################################################################
-2019-11-16: import of UCSC GENCODE group processing of GENCODE VM24 (markd)
-    # PRE-RELEASE
-
+2019-11-16: import of UCSC GENCODE group processing of GENCODE VM24 PRE-RELEASE (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
 
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24
     pushd /hive/data/genomes/mm10/bed/gencodeVM24
 
     (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/gencodeGenerateTrackDbs mm10 M24 99 'Nov 2019'
 
@@ -18431,15 +18429,51 @@
     #	real    101m20.296s
 
     cat fb.regenCho1.chainMm10Link.txt
     #	1522181082 bases of 2266312740 (67.166%) in intersection
     cat fb.regenCho1.chainSynMm10Link.txt
     #   1397889394 bases of 2266312740 (61.681%) in intersection
 
     time (doRecipBest.pl -load -workhorse=hgwdev regenCho1 mm10 \
       -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 &
     # real    660m29.571s
 
     cat fb.regenCho1.chainRBest.Mm10.txt
     # 1396267649 bases of 2266312740 (61.610%) in intersection
 
 ##############################################################################
+2020-01-16: import of UCSC GENCODE group processing of GENCODE VM24 (markd)
+    # deprecate pre-release
+    mv /hive/data/genomes/mm10/bed/gencodeVM24 /hive/data/genomes/hg38/bed/gencodeVM24pre
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24
+    pushd /hive/data/genomes/mm10/bed/gencodeVM24
+
+    (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/gencodeGenerateTrackDbs mm10 M24 99 'Jan 2020'
+
+    # If being pushed public, update 'Release Notes' in
+    # mouse/mm10/wgEncodeGencodeSuper.html
+
+    # edit human/mm10/trackDb.gencode.ra to add new .ra file include
+    make DBS=mm10
+
+    ## only if being pushed to RR:
+    # edit all.joiner to add ~/tmp/gencodeVM24.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm10/bed/gencodeVM24
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=mm10 alpha
+    # if pushing public: add ticket and MARK QA READY
+
+##############################################################################