1fd6ea4cb6bef2161c5fa1d951a8594d70eadcc9
markd
  Tue Apr 9 15:10:40 2019 -0700
import of GENCODE V30, V30lift37 and VM21

diff --git src/hg/makeDb/doc/mm10.txt src/hg/makeDb/doc/mm10.txt
index 99e7fac..4c10ba7 100644
--- src/hg/makeDb/doc/mm10.txt
+++ src/hg/makeDb/doc/mm10.txt
@@ -17869,15 +17869,50 @@
     zcat exonNuc/c*.gz | gzip -c > $gp.$mz.exonNuc.fa.gz &
     # about 6 minutes
 
     rm -rf exonAA exonNuc
 
     export mz=multiz60way
     export gp=knownCanonical
     export db=mm10
     export pd=/usr/local/apache/htdocs-hgdownload/goldenPath/$db/$mz/alignments
     mkdir -p $pd
     ln -s `pwd`/$gp.$mz.exonAA.fa.gz $pd/$gp.exonAA.fa.gz
     ln -s `pwd`/$gp.$mz.exonNuc.fa.gz $pd/$gp.exonNuc.fa.gz
 
     cd  $pd
     md5sum *.fa.gz > md5sum.txt
+##############################################################################
+2019-04-08: import of UCSC GENCODE group processing of GENCODE VM20 (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/gencodeVM21
+    pushd /hive/data/genomes/mm10/bed/gencodeVM21
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    ##  gencode-cmp.tsv check to see if sizes make sense
+
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M21 96 'Apr 2019'
+
+    ## only if being pushed to RR:
+    # Update mouse/mm10/wgEncodeGencodeSuper.html
+    # Update 'Release Notes' to describe new release.
+
+    # 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/gencodeVM21.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm10/bed/gencodeVM21
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10
+
+    # commit all and make push request, the file tables.lst will have the
+    # list of tables for the push request.
+
+    cd ~/kent/src/hg/makeDb/trackDb
+    make alpha DBS=mm10
+
+#########################################################################