1fe89284953dd069f7155892bdcb8306adea13ef
markd
  Thu Nov 3 21:31:54 2022 -0700
import of v42lift37

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index 7c3c8a6..2f746e6 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -1051,15 +1051,75 @@
     pushd ~/kent/src/hg/makeDb/trackDb
     ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs hg19 41lift37 107 'July 2022'
 
     # edit human/hg19/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=hg19
 
     # edit  all.joiner to add ~/tmp/gencodeV41lift37.joiner
     # verify with:
     pushd /hive/data/genomes/hg19/bed/gencodeV41lift37/hgcImport
     make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # commit all
     jkmake alpha DBS=hg19
 
 ##############################################################################
+2022-07-12: import of UCSC GENCODE group processing of GENCODE V41lift37 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/gencodeV41lift37/hgcImport
+    pushd /hive/data/genomes/hg19/bed/gencodeV41lift37/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
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs hg19 41lift37 107 'July 2022'
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV41lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV41lift37/hgcImport
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+    jkmake alpha DBS=hg19
+
+##############################################################################
+2022-11-03: import of UCSC GENCODE group processing of GENCODE V42lift37 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/gencodeV42lift37/hgcImport
+    pushd /hive/data/genomes/hg19/bed/gencodeV42lift37/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
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs hg19 42lift37 108 'Oct 2022'
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+
+    # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
+    # to describe new release.
+
+    jkmake DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV42lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV42lift37/hgcImport
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # commit all
+    jkmake alpha DBS=hg19
+
+##############################################################################