7fb2f3f334694376f7bec47237552ddf8eb186dc
markd
  Wed Apr 26 10:13:42 2023 -0700
import of gencode VM33 prerelease

diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt
index 18ab4f5..77f1fe4 100644
--- src/hg/makeDb/doc/mm39/gencode.txt
+++ src/hg/makeDb/doc/mm39/gencode.txt
@@ -1,343 +1,377 @@
 ##############################################################################
 2021-03-12: import of UCSC GENCODE group processing of GENCODE VM26 (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM26
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
 
     (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/gencodeGenerateTrackDbsOldSchema mm39 M26 103 'Feb 2021'
 
     # If being pushed public, update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM26.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM26
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
        Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
 2021-06-29: import of UCSC GENCODE group processing of GENCODE VM27 (markd)
     update from pre-release
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM27
     pushd /hive/data/genomes/mm39/bed/gencodeVM27
 
     (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/gencodeGenerateTrackDbsOldSchema mm39 M27 104 'May 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM27.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM27
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
 2021-10-15: import of UCSC GENCODE group processing of GENCODE VM28 pre-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/mm39/bed/gencodeVM28/hgcImportPre
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
 
     (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 mm39 M28 105 'Oct 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImportPre.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # if pushing public: add ticket and MARK QA READY
 
 ##############################################################################
 2022-01-16: import of UCSC GENCODE group processing of GENCODE VM28 final (markd)
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
 
     (time nice make -kO -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 mm39 M28 105 'Oct 2021'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM28/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # however, these are not currently used by the browser, so modify joiner check. Check
     # with GENCODE is this is expected, might be a cleanup on move to mm39
 
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
     # add ticket and MARK QA READY
 
 ##############################################################################
 2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 pre-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/mm39/bed/gencodeVM29/hgcImportPre
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
 
     (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 mm39 M29 106 'Feb 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM29/hgcImportPre.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
 2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 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/mm39/bed/gencodeVM29/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/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 mm39 M29 106 'Feb 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM29/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
 2022-05-13: import of UCSC GENCODE group processing of GENCODE VM30 pre-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/mm39/bed/gencodeVM30/hgcImportPre
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
 
     (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 mm39 M30 107 'June 2022'
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include  as alpha
     jkmake DBS=mm39
 
     # edit all.joiner to add ~/tmp/gencodeVM30.joiner
 
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     make DBS=mm39 alpha
 ##############################################################################
 2022-07-12: import of UCSC GENCODE group processing of GENCODE VM30 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/mm39/bed/gencodeVM30/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/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 mm39 M30 107 'July 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM30/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
 2022-11-03: import of UCSC GENCODE group processing of GENCODE VM31 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/mm39/bed/gencodeVM31/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport
 
     # get initial version of transcript_rankings,
     http://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_mouse/release_M31/gencode.vM31.transcript_rankings.txt.gz
 
     (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 mm39 M31 108 'Oct 2022'
 
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # edit all.joiner to add ~/tmp/gencodeVM31/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
-2022-12-29: import of UCSC GENCODE group processing of GENCODE VM31 pre-release (markd)
-2023-02-13: import of UCSC GENCODE group processing of GENCODE VM31 final release (markd)
+2022-12-29: import of UCSC GENCODE group processing of GENCODE VM32 pre-release (markd)
+2023-02-13: import of UCSC GENCODE group processing of GENCODE VM32 final release (markd)
 
     pre-release moved to hgcImportPre, notes revised
     
 
     # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
     # download, build and load tables
     mkdir -p /hive/data/genomes/mm39/bed/gencodeVM32/hgcImport
     pushd /hive/data/genomes/mm39/bed/gencodeVM32/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 mm39 M32 109 'Feb 2023'
 
     # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
     jkmake DBS=mm39
 
     ## only if being pushed to RR:
     # Update 'Release Notes' in
     # mouse/mm39/wgEncodeGencodeSuper.html
 
     # edit all.joiner to add ~/tmp/gencodeVM32/hgcImport.joiner
     # verify with:
     pushd /hive/data/genomes/mm39/bed/gencodeVM32/hgcImport
     make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
 
     # check tracks in browser sandbox
     # commit all
     jkmake DBS=mm39 alpha
 ##############################################################################
+2023-04-25: import of UCSC GENCODE group processing of GENCODE VM33 pre-release (markd)
+
+    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
+    pre="Pre"
+
+    # download, build and load tables
+    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre}
+    pushd /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${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 mm39 M33 110 'May 2023'
+
+    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
+    jkmake DBS=mm39
+
+    ## only if being pushed to RR:
+    # Update 'Release Notes' in
+    # mouse/mm39/wgEncodeGencodeSuper.html
+
+    # edit all.joiner to add ~/tmp/gencodeVM33/hgcImport${pre}.joiner
+    # verify with:
+    pushd /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre}
+    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck
+
+    # check tracks in browser sandbox
+    # commit all
+    jkmake DBS=mm39 alpha
+##############################################################################