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

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 4773af7..1242d00 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -619,15 +619,50 @@
     # 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/gencodeV33.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV33
     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
 
 #########################################################################
+2020-03-11: import of UCSC GENCODE group processing of GENCODE V34 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/hg38/bed/gencodeV34Pre
+    pushd /hive/data/genomes/hg38/bed/gencodeV34Pre
+
+    (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 hg38 34 100 'Mar 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/gencodeV34.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV34Pre
+    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
+
+#########################################################################