ca39d76b0c4deafcb785e8bea631d316b3bb59ed
markd
  Fri Oct 28 21:28:51 2022 -0700
import of GENCODE V42 final release with addition of transcript rankings

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index 807e730..9deeec4 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -1108,15 +1108,51 @@
     # add to human/hg38/trackDb.gencode.ra
 
     # edit all.joiner to add ~/tmp/gencodeV42.joiner
 
     jkmake DBS=hg38
 
     # check joiner 
     pushd /hive/data/genomes/hg38/bed/gencodeV42Pre/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
 
 #########################################################################
+2022-10-28: import of UCSC GENCODE group processing of GENCODE V42 final release 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/gencodeV42/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV42/hgcImport
+
+    # get initial version of transcript_rankings,
+    # http://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_human/release_42/gencode.v42.transcript_rankings.txt.gz
+    
+    (time nice make -O -j 32 -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/gencodeGenerateTrackDbs hg38 42 107 'Oct 2022'
+
+    # Update 'Release Notes' (for final)
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to remove alpha
+
+    # edit all.joiner to add ~/tmp/gencodeV42.joiner
+
+    jkmake DBS=hg38
+
+    # check joiner 
+    pushd /hive/data/genomes/hg38/bed/gencodeV42/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+