1de6d513b0f0fdd55dee82f8f4dd2cd14bfb349f
markd
  Thu Jan 11 19:13:08 2024 -0800
import of gencode 45lift37

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index 859653e..8a497f5 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -1223,15 +1223,55 @@
     # edit  all.joiner to add ~/tmp/gencodeV45lift37.joiner
     # verify with:
     pushd /hive/data/genomes/hg19/bed/gencodeV45lift37/hgcImport${pre}
     make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
       These two complaint are cause by the new PAR id scheme causing a chrY V19 copy to be brought in.
       This needs to fixed in some way
       Error: 1 duplicates in hg19.wgEncodeGencodeTranscriptSourceV45lift37.transcriptId including 'ENST00000302805.2'
       Error: 1 duplicates in hg19.for this release.
 
 
     # commit all
     jkmake alpha DBS=hg19
 
 ##############################################################################
+2024-01-11: import of UCSC GENCODE group processing of GENCODE V45lift38 final release (markd)
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    # set shell variable:
+    pre=""
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/hg19/bed/gencodeV45lift37/hgcImport${pre}
+    pushd /hive/data/genomes/hg19/bed/gencodeV45lift37/hgcImport{pre}
+
+    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&
+
+    # compare tables from previous release to see if number changed makes
+    # sense.  Results are in gencode-cmp.tsv
+    # generate trackDb and joiner blurb
+    pushd ~/kent/src/hg/makeDb/trackDb
+    ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs hg19 45lift37 111 'Jan 2024'
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    # edit all.joiner to add ~/tmp/gencodeV45lift37.joiner
+
+    # Update human/hg19/wgEncodeGencodeSuper.html and update 'Release Notes'
+    # to describe new release.
+
+    jkmake DBS=hg19
+
+    # edit  all.joiner to add ~/tmp/gencodeV45lift37.joiner
+    # verify with:
+    pushd /hive/data/genomes/hg19/bed/gencodeV45lift37/hgcImport${pre}
+    make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+      These two complaint are cause by the new PAR id scheme causing a chrY V19 copy to be brought in.
+      This needs to fixed in some way
+      Error: 1 duplicates in hg19.wgEncodeGencodeTranscriptSourceV45lift37.transcriptId including 'ENST00000302805.2'
+      Error: 1 duplicates in hg19.for this release.
+
+
+    # commit all
+    jkmake alpha DBS=hg19
+
+##############################################################################