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

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 6f32558..47b51f2 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33323,15 +33323,44 @@
 cat /hive/data/outside/hgmd/2018.4-hgmd-public_hg38.tsv | cut -f7 | sort -u > hgmdTranscripts.txt
 zcat process/hg19.curated.gp.gz | fgrep -f hgmdTranscripts.txt - > hgmd.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqHgmd hgmd.curated.gp
 #############################################################################
 # genomenom mastermind track, Max, Feb 2019
 cd /hive/data/genomes/hg19/bed/mastermind/
 wget 'https://mastermind.genomenon.com/cvr/download?format=csv' -O - > mastermind.2018.11.26.csv.gz
 unzip mastermind.2018.11.26.csv.zip
 mv mastermind_cited_variants_reference-2018.11.26-csv/ 2018-11-26
 hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > chromAlias.tab
 python ~/kent/src/hg/makeDb/mastermind/mastermindToBed.py 2018-11-26/mastermind_cited_variants_reference-2018.11.26.csv 
 bedSort mastermind.bed mastermind.bed
 bedToBigBed -type=bed9+ -as=~/kent/src/hg/makeDb/mastermind/mastermind.as -tab mastermind.bed /hive/data/genomes/hg19/chrom.sizes  mastermind.bb
 ln -s `pwd`/mastermind.bb /gbdb/hg19/bbi/mastermind.bb
 #############################################################################
+2019-04-08: import of UCSC GENCODE group processing of GENCODE V30lift37 (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg19/bed/gencodeV30lift37
+    pushd /hive/data/genomes/hg19/bed/gencodeV30lift37
+    (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 hg19 30lift37 96 'Apr 2019'
+
+    # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
+    # to describe new release. [ONLY if it's going to be pushed]
+
+    # edit human/hg19/trackDb.wgEncode.ra to add new .ra file include
+    make DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV30lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV30lift37
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+
+##############################################################################