be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 315a57f..0e05a33 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -725,15 +725,83 @@
     ../../makeDb/outside/gencode/bin//gencodeGenerateTrackDbs hg38 36 102 'November 2020'
 
     # edit human/hg38/trackDb.gencode.ra to add new .ra file include
     make DBS=hg38
 
     # edit all.joiner to add ~/tmp/gencodeV36.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV36
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     # SKIP FOR NOW, hgc needs to handle these for testing on hgwdev
     # make DBS=hg38 alpha
 #########################################################################
+2020-12-19: import of UCSC GENCODE group processing of GENCODE V35 for hgc all gencode  (markd)
+    # due to delays in hgGene work, create hgc version
+    
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg38/bed/gencodeV35/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV35/hgcImport
+
+    (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
+    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 35 101 'Aug 2020'
+
+    # Update 'Release Notes' in if pushing public
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    make DBS=hg38
+
+    ## only if being pushed to RR (may be there from pre-release)
+    # edit all.joiner to add ~/tmp/gencodeV35.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV35/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=hg38 alpha
+    # if pushing public: create ticket and MARK QA READY
+#########################################################################
+2020-12-20: import of UCSC GENCODE group processing of GENCODE V36 for hgc all gencode  (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg38/bed/gencodeV36/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV36/hgcImport
+
+    (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
+    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 36 102 'Nov 2020'
+
+    # Update 'Release Notes' in if pushing public
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    make DBS=hg38
+
+    ## only if being pushed to RR (may be there from pre-release)
+    # edit all.joiner to add ~/tmp/gencodeV36.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV36/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    make DBS=hg38 alpha
+    # if pushing public: create ticket and MARK QA READY
+#########################################################################