fcdf5c401c80840d28c346409c4fbb527544fac7
markd
  Tue Jun 9 13:59:33 2020 -0700
make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index 6d4e14c..aed0afd 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -673,15 +673,44 @@
     # edit human/hg19/trackDb.gencode.ra to add new .ra file include
     make DBS=hg19
 
     # edit  all.joiner to add ~/tmp/gencodeV34lift37.joiner
     # verify with:
     pushd /hive/data/genomes/hg19/bed/gencodeV34lift37Pre
     make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # commit all
 ###
 2020-03-11: final release (markd)
     mkdir -p /hive/data/genomes/hg19/bed/gencodeV34lift37
   repeat above, only making release month April
     ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg19 34lift37 100 'April 2020'
 
+##############################################################################
+2020-06-07: import of UCSC GENCODE group processing of GENCODE V35lift37 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/hg19/bed/gencodeV35lift37Pre
+    pushd /hive/data/genomes/hg19/bed/gencodeV35lift37Pre
+    (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 35lift37 101 'June 2020'
+
+    # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
+    # to describe new release.
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    make DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV35lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV35lift37Pre
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+##############################################################################