db0877a0f789518c170e95923feee7ad95e15b55
markd
  Sun Mar 22 09:14:47 2020 -0700
import of GENCODE V34 and VM25 prereleases

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index d948950..1a1a7be 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -18476,16 +18476,49 @@
     make DBS=mm10 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
 clinvar lift, done, Fri Jan 31 06:12:46 PST 2020, max
 doClinvarLift mm10
 featureBits hg38 clinvarLift.bed
 620623 bases of 3095998939 (0.020%) in intersection
 wc -l clinvarLift.bed
 610774 clinvarLift.bed
 featureBits mm10 clinvarLift.mm10.bed
 581378 bases of 2652783500 (0.022%) in intersection
 wc -l clinvarLift.mm10.bed
 575023 clinvarLift.mm10.bed
 ##############################################################################
+2020-03-11: import of UCSC GENCODE group processing of GENCODE VM25 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/gencodeVM25Pre
+    pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre
+
+    (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 M25 100 'March 2020'
+
+    # If being pushed public, update 'Release Notes' if pushing puyblic.
+    # mouse/mm10/wgEncodeGencodeSuper.html
 
+    # edit mouse/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/gencodeVM25.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre
+    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
+
+##############################################################################