##############################################################################
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 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"

2023-04-25: import of UCSC GENCODE group processing of GENCODE VM33 final release (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
    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 'July 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
##############################################################################
2023-04-25: import of UCSC GENCODE group processing of GENCODE VM34 pre-release (markd)

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
    # set shell variable:
    pre="Pre"

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${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 M34 111 'Nov 2023'

    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include

    ## only if being pushed to RR:
    # Update 'Release Notes' in
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner
    # verify with:
    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=mm39 alpha
##############################################################################
2024-01-11: import of UCSC GENCODE group processing of GENCODE VM34 final elease (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/mm39/bed/gencodeVM34/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${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 M34 111 'Jan 2024'

    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include

    ## only if being pushed to RR:
    # Update 'Release Notes' in
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner
    # already added for pre-release
    # verify with:
    pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=mm39 alpha
##############################################################################
2024-03-04: import of UCSC GENCODE group processing of GENCODE VM35 pre-release (markd)

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
    # set shell variable:
    pre="Pre"

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${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 M35 112 'April 2024'

    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include

    ## only if being pushed to RR:
    # Update 'Release Notes' in
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    # edit all.joiner to add ~/tmp/gencodeVM35/hgcImport${pre}.joiner
    # already added for pre-release
    # verify with:
    pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=mm39 alpha
##############################################################################
2024-07-31: import of UCSC GENCODE group processing of GENCODE VM36 pre-release for GENCODE Versions (markd)
2024-10-17: import of final release

   # set shell variable:
   # pre-release shell variables 
       ver=M36
       ensver=113
       pre="Pre"
       ensdate='Sept 2024 pre-release' 
   # release shell variables 
       ver=M36
       ensver=113
       pre=""
       ensdate='Oct 2024'

    # 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/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${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 ${ver} ${ensver} "${ensdate}"

    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner

    # if final release, Update 'Release Notes' 
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    pushd /hive/data/genomes/mm39/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=mm39 alpha
##############################################################################
2025-02-05: import of UCSC GENCODE group processing of GENCODE VM37 pre-release for GENCODE Versions (markd)
2025-05-31: final release

   # set shell variable:
   # pre-release shell variables 
       ver=M37
       ensver=114
       pre="Pre"
       ensdate='Feb 2025 pre-release' 
   # release shell variables 
       ver=M37
       ensver=114
       pre=""
       ensdate='May 2025'

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${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 ${ver} ${ensver} "${ensdate}"

    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner

    # if final release, Update 'Release Notes' 
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    pushd
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all

    jkmake DBS=mm39 alpha
##############################################################################
2025-07-29: import of UCSC GENCODE group processing of GENCODE VM38 pre-release for GENCODE Versions (markd)
2025-09-08: import of UCSC GENCODE group processing of GENCODE VM38 release for GENCODE Versions (markd)

   # set shell variable:
   # pre-release shell variables 
       ver=M38
       ensver=115
       pre="Pre"
       ensdate='July 2025 pre-release' 
   # release shell variables 
       ver=M38
       ensver=115
       pre=""
       ensdate='Sept 2025'

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${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 ${ver} ${ensver} "${ensdate}"


    # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner

    # if final release, Update 'Release Notes' 
    # mouse/mm39/wgEncodeGencodeSuper.html

    jkmake DBS=mm39

    pushd
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all

    jkmake DBS=mm39 alpha
##############################################################################
