cb95ab0ac3de81c54babc8b9ba1326d93901ad96
markd
  Fri Apr 22 09:27:25 2022 -0700
import of All GENCODE V40

diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt
index ea53c4e..8c8c1f4 100644
--- src/hg/makeDb/doc/hg38/gencode.txt
+++ src/hg/makeDb/doc/hg38/gencode.txt
@@ -970,16 +970,58 @@
     # Update 'Release Notes' (for final)
     # human/hg38/wgEncodeGencodeSuper.html
 
     # edit human/hg38/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=hg38
 
     # edit all.joiner to add ~/tmp/gencodeV40.joiner
     # verify with:
     pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=hg38 alpha
 #########################################################################
+2022-04-21: import of UCSC GENCODE group processing of GENCODE V40 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/gencodeV40/hgcImport
+    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImport
+
+    (time nice make -O -j 32 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # reported stray space in
+    release_40/gencode.v40.metadata.Pubmed_id.gz
+
+    # compare tables from previous release to see if number changed makes
+    diff -qr ../hgcImportPre/tables tables
+    Files ../hgcImportPre/tables/wgEncodeGencodeAttrsV40.tab and tables/wgEncodeGencodeAttrsV40.tab differ
+    Files ../hgcImportPre/tables/wgEncodeGencodeTagV40.tab and tables/wgEncodeGencodeTagV40.tab differ
+    cmp <(sort ../hgcImportPre/tables/wgEncodeGencodeAttrsV40.tab) <(sort tables/wgEncodeGencodeAttrsV40.tab)
+    cmp <(sort ../hgcImportPre/tables/wgEncodeGencodeTagV40.tab) <(sort tables/wgEncodeGencodeTagV40.tab)
+    # Due to sorting differences; code has already been change to sort these for the future
+
+    # 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 40 106 'Feb 2022'
+
+    # Update 'Release Notes' (for final)
+    # human/hg38/wgEncodeGencodeSuper.html
+
+    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=hg38
+
+    # edit all.joiner to add ~/tmp/gencodeV40.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImport
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg38 alpha
+#########################################################################