0f6f8c5cdfc1c5385c814102a4fa59afb08d2849
markd
  Wed Jul 31 23:45:27 2024 -0700
import of GENCODE v47, v47lift37, and vM36 pre-releases

diff --git src/hg/makeDb/doc/hg19.gencode.txt src/hg/makeDb/doc/hg19.gencode.txt
index cb9d3b1..838c5b1 100644
--- src/hg/makeDb/doc/hg19.gencode.txt
+++ src/hg/makeDb/doc/hg19.gencode.txt
@@ -1313,15 +1313,62 @@
     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 are now fixed by filter and input time.
 
     # commit all
     jkmake alpha DBS=hg19
 
 2024-05-15 - EBI got a fixed version of gencode.v46lift37.metadata.HGNC.gz,
 which will also have all symbols mapped to HGNC ids.
 
 download 
   https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/GRCh37_mapping/gencode.v46lift37.metadata.HGNC.gz
 to data/release_46lift37/ and rerun the make
 ##############################################################################
+2024-07-31: import of UCSC GENCODE group processing of GENCODE V47lift38 pre-release for GENCODE Versions (markd)
+
+   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release type and versions
+
+   # pre-release shell variables 
+       ver=47lift37
+       ensver=113
+       pre="Pre"
+       ensdate='Sept 2024 pre-release' 
+   # release shell variables 
+       ver=47lift37
+       ensver=113
+       pre=""
+       ensdate='Sept 2024' 
+    
+
+    # 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/gencodeV${ver}/hgcImport${pre}
+    pushd /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}p
+
+    (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 hg19 ${ver} ${ensver} "${ensdate}"
+
+    # edit human/hg19/trackDb.gencode.ra to add new .ra file include
+    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner
+
+    # if final release, Update 'Release Notes' 
+    #  human/hg19/wgEncodeGencodeSuper.html
+
+    jkmake DBS=hg19
+
+    # check joiner 
+    pushd /hive/data/genomes/hg19/bed/gencodeV${ver}/hgcImport${pre}
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=hg19 alpha
+#########################################################################