##############################################################################
2013-12-13: import of UCSC GENCODE group processing of GENCODE VM2 (markd)
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM2
    cd /hive/data/genomes/mm10/bed/gencodeVM2

    # create Makefile from previous one.
    cp /hive/data/genomes/hg19/bed/gencodeV19/Makefile .

    # download, build and load tables
    (time nice make -j 10) >&build.1.out&

    # compare tables from previous release to see if number changed makes
    # sense.
        # NOT DONE THIS TIME, SINCE THIS is the first mouse.
        make cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.
    ## Important to make sure filter attrs.transcriptType matches current set
    ## figured out with
    select distinct transcriptType from wgEncodeGencodeAttrsVM2 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM2.ra
    cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM2.html

    # edit these plus human/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM2.ra in reverse order with previous
    #   tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous -0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers
    ### track handler for this version of gencode:
    registerTrackHandler("wgEncodeGencodeVM2", gencodeGeneMethods);

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    cd /hive/data/genomes/mm10/bed/gencodeVM2
    make joinerCheck
    # see output in check/joiner.out
##############################################################################
# 2014-08-17: import of UCSC GENCODE group processing of GENCODE VM3 (markd)

    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM3/data
    cd /hive/data/genomes/mm10/bed/gencodeVM3

    # download gencode release
    cd data
    wget -nv -r -np ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3
    mv ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3 .
    rm -rf ftp.sanger.ac.uk

    cd ..
    # create Makefile from previous one.
    cp /hive/data/genomes/mm10/bed/gencodeVM2/Makefile .

    # build and load tables
    (time nice make -j 10) >&build.1.out&

    # compare tables from previous release to see if number changed makes
    # sense.
        make cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.
    ## Important to make sure filter attrs.transcriptType matches current set
    ## figured out with
    select distinct transcriptType from wgEncodeGencodeAttrsVM3 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM3.ra
    cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM3.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM3.ra in reverse order with previous
    #   tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers
    ### track handler for this version of gencode:
    registerTrackHandler("wgEncodeGencodeVM3", gencodeGeneMethods);

    # update all.joiner and validate
    # look for the last section `begin Gencode VM?' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    cd /hive/data/genomes/mm10/bed/gencodeVM3
    make joinerCheck  # output in check/joiner.out

############################################################################
# 2014-12-05: import of UCSC GENCODE group processing of GENCODE VM4 (markd)

    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM4/data
    cd /hive/data/genomes/mm10/bed/gencodeVM4

    # create Makefile from previous one.
    # WARNING: next build start with hg/makeDb/outside/gencode/gencodeLoad.mk
    cp  /hive/data/genomes/hg38/bed/gencodeV21/Makefile .

    # download, build and load tables
    (time nice make -j 10) >&build.1.out&

    # compare tables from previous release to see if number changed makes
    # sense.
        make cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.
    ## Important to make sure filter attrs.transcriptType matches current set
    ## figured out with
    select distinct transcriptType from wgEncodeGencodeAttrsVM4 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM4.ra
    cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM4.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM4.ra in reverse order with previous
    #   tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers
    ### track handler for this version of gencode:
    registerTrackHandler("wgEncodeGencodeVM4", gencodeGeneMethods);

    # update all.joiner and validate
    # look for the last section `begin Gencode VM?' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    cd /hive/data/genomes/mm10/bed/gencodeVM4
    make joinerCheck  # output in check/joiner.out

#########################################################################
2015-06-29-13: import of UCSC GENCODE group processing of GENCODE VM5 (markd)
    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM5
    cd /hive/data/genomes/mm10/bed/gencodeVM5

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set
    # release and transcript support versions


    # download, build and load tables
    (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.
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.
    ## Important to make sure filter attrs.transcriptType matches current set
    ## figured out with
    select distinct transcriptType from wgEncodeGencodeAttrsVM5 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM5.ra
    cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM5.html

    # edit these plus human/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM5.ra in reverse order with previous
    #   tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM5
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2015-10-02: import of UCSC GENCODE group processing of GENCODE VM7 (markd)
    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM7
    cd /hive/data/genomes/mm10/bed/gencodeVM7

    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set
    # release and transcript support versions


    # download, build and load tables
    (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.
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructiuons in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM4.ra mouse/mm10/wgEncodeGencodeVM7.ra
    cp mouse/mm10/wgEncodeGencodeVM4.html mouse/mm10/wgEncodeGencodeVM7.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM7.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM7
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2016-03-14: import of UCSC GENCODE group processing of GENCODE VM8 (markd)
# not to be pushed to RR

    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM8
    cd /hive/data/genomes/mm10/bed/gencodeVM8

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

    # download, build and load tables
    (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.
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructions in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM7.ra mouse/mm10/wgEncodeGencodeVM8.ra
    cp mouse/mm10/wgEncodeGencodeVM7.html mouse/mm10/wgEncodeGencodeVM8.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM8.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM8
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2016-03-14: import of UCSC GENCODE group processing of GENCODE VM9 (markd)

    # download files
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM9
    cd /hive/data/genomes/mm10/bed/gencodeVM9

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

    # download, build and load tables
    (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.
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructions in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM9.ra
    cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM9.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM9.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM9
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2016-07-22: import of UCSC GENCODE group processing of GENCODE VM10 (markd)
    # will not be pushed to the RR.

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM10
    pushd /hive/data/genomes/mm10/bed/gencodeVM10
    (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

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructions in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM9.ra mouse/mm10/wgEncodeGencodeVM10.ra
    cp mouse/mm10/wgEncodeGencodeVM9.html mouse/mm10/wgEncodeGencodeVM10.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM10.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.  [ONLY if it's going to be pushed]

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM10
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2016-10-27: import of UCSC GENCODE group processing of GENCODE VM11 (markd)

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM11
    cd /hive/data/genomes/mm10/bed/gencodeVM11
    (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.
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructions in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM11.ra
    cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM11.html

    # edit these plus mouse/mm10/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeVM11.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM11
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

##############################################################################
2016-12-08: import of UCSC GENCODE group processing of GENCODE VM12 (markd)
            No being pushed to RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM12
    cd /hive/data/genomes/mm10/bed/gencodeVM12
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv- check to see if sizes make sense

    ## Copy and update trackDb files from previous release.
    ## Change version and use lower priority so it sorts to top of
    ## super track page.  Follow instructions in ra file to ensure
    ## filters are correct.
    cd kent/src/hg/makeDb/trackDb
    cp mouse/mm10/wgEncodeGencodeVM11.ra mouse/mm10/wgEncodeGencodeVM12.ra
    cp mouse/mm10/wgEncodeGencodeVM11.html mouse/mm10/wgEncodeGencodeVM12.html

    # edit these plus mouse/mm10/trackDb.ra
    # - set priorities in wgEncodeGencodeVM12.ra tracks so newest shows up first
    #     priority - set to previous version priority minus 0.001
    #     searchPriority - set each to previous minus 0.001
    # - make current track default to pack and hide previous [ONLY if it's going to be pushed]
    #     superTrack wgEncodeGencodeSuper pack
    # - Update wgEncodeGencodeSuper.html to describe new release and to
    #   pick up other updates.

    # DID NOT UPDATE all.joiner SINCE NOT BEING PUSHED PUBLIC
    # update all.joiner and validate
    # look for the last section `begin Gencode V??' in all.joiner
    # and copy and update version
    # repeat this until happy, editing minCheck as needed
    # output in check/joiner.out
    cd /hive/data/genomes/mm10/bed/gencodeVM12
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2017-04-16: import of UCSC GENCODE group processing of GENCODE VM13 (markd)

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM13
    pushd /hive/data/genomes/mm10/bed/gencodeVM13
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M13 88 'March 2017'

    # edit mouse/mm10/trackDb.ra to add new .ra file include
    make DBS=mm10

    # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit  all.joiner to add ~/tmp/gencodeVM13.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM13
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all
##############################################################################
2017-05-31: import of UCSC GENCODE group processing of GENCODE VM14 (markd)

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM14
    pushd /hive/data/genomes/mm10/bed/gencodeVM14
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M14 89 'May 2017'

    # edit mouse/mm10/trackDb.wgEncode.ra to add new .ra file include
    make DBS=mm10

    # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit  all.joiner to add ~/tmp/gencodeVM14.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM14
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all
##############################################################################
2017-09-15: import of UCSC GENCODE group processing of GENCODE VM15 (markd)
    # not to push to the RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM15
    pushd /hive/data/genomes/mm10/bed/gencodeVM15
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M15 90 'Aug 2017'

    # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM15.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM15
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all

##############################################################################
2017-12-17: import of UCSC GENCODE group processing of GENCODE VM16 (markd)
    # being push to the RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM16
    pushd /hive/data/genomes/mm10/bed/gencodeVM16
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017'

    # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM16.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM16
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

#########################################################################
2018-03-08: update UCSC GENCODE VM16 to include protein id (for VAI) and fix PAR tag

cd /hive/data/genomes/mm10/bed/gencodeVM16

# save existing data
mkdir -p prev/pre-proteinId
mv tables/wgEncodeGencodeAttrsVM16.tab tables/wgEncodeGencodeTagVM16.tab prev/pre-proteinId/
mv loaded/wgEncodeGencodeAttrsVM16.tab.loaded loaded/wgEncodeGencodeTagVM16.tab.loaded prev/pre-proteinId/
mv data/gencode.tsv prev/pre-proteinId/
cp -p data/gencode.vM16.transcriptionSupportLevel.tab prev/pre-proteinId/

# edit gencodeLoad.mk to set mm10 as target

# get gencode.tsv without rebuild TSL file or loading tables that don't change
~markd/compbio/ccds/ccds2/output/bin/x86_64/opt/gencodeGxfToAttrs --keepGoing data/release_M16/gencode.vM16.chr_patch_hapl_scaff.annotation.gtf.gz data/gencode.tsv
make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk   loaded/wgEncodeGencodeAttrsVM16.tab.loaded  loaded/wgEncodeGencodeTagVM16.tab.loaded

# 2018-03-19: update search to include protein id
cd kent/src/hg/makeDb/trackDb
../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017'

#########################################################################
2018-07-01: import of UCSC GENCODE group processing of GENCODE VM17 (markd)
    # not being push to the RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM17
    pushd /hive/data/genomes/mm10/bed/gencodeVM17
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M17 92 'Mar 2018'

    ## only if being pushed to RR:
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM17.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM17
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

##############################################################################
2018-08-03: import of UCSC GENCODE group processing of GENCODE VM18 (markd)
    # being push to the RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM18
    pushd /hive/data/genomes/mm10/bed/gencodeVM18
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M18 93 'July 2018'

    ## only if being pushed to RR:
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM18.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM18
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

    cd ~/kent/src/hg/makeDb/trackDb
    make alpha DBS=mm10

#########################################################################
2018-11-10: import of UCSC GENCODE group processing of GENCODE VM19 (markd)
    # not being push to the RR

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM19
    pushd /hive/data/genomes/mm10/bed/gencodeVM19
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M19 94 'Oct 2018'

    ## only if being pushed to RR:
    (skipped)
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR: (SKIPPED)
    # edit  all.joiner to add ~/tmp/gencodeVM19.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM19
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

    cd ~/kent/src/hg/makeDb/trackDb
    make alpha DBS=mm10

##############################################################################
2018-11-30: import of UCSC GENCODE group processing of GENCODE VM20 prerelease (markd)
    # This is a prerelease for testing and is *not* to pushed until the final release.

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM20
    pushd /hive/data/genomes/mm10/bed/gencodeVM20
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M20 95 'Dec 2018'

    ## only if being pushed to RR:
    (skipped)
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR: (SKIPPED)
    # edit  all.joiner to add ~/tmp/gencodeVM20.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM20
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

    cd ~/kent/src/hg/makeDb/trackDb
    make alpha DBS=mm10

##############################################################################
2019-04-08: import of UCSC GENCODE group processing of GENCODE VM20 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM21
    pushd /hive/data/genomes/mm10/bed/gencodeVM21
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M21 96 'Apr 2019'

    ## only if being pushed to RR:
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM21.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM21
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

    cd ~/kent/src/hg/makeDb/trackDb
    make alpha DBS=mm10

    # commit all
    # if pushing public, add ticket and MARK QA READY

#########################################################################
2019-07-03: import of UCSC GENCODE group processing of GENCODE VM22 (markd)
    # Replaced import of 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/mm10/bed/gencodeVM22
    pushd /hive/data/genomes/mm10/bed/gencodeVM22
    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    ##  gencode-cmp.tsv check to see if sizes make sense

    # generate trackDb and joiner blurb
    pushd ~/kent/src/hg/makeDb/trackDb
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M22 97 'June 2019'

    ## only if being pushed to RR:
    # Update mouse/mm10/wgEncodeGencodeSuper.html
    # Update 'Release Notes' to describe new release.

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit  all.joiner to add ~/tmp/gencodeVM22.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM22
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10

    # commit all and make push request, the file tables.lst will have the
    # list of tables for the push request.

    cd ~/kent/src/hg/makeDb/trackDb
    make alpha DBS=mm10

    # commit all
    # if pushing public, add ticket and MARK QA READY

##############################################################################
2019-08-30: import of UCSC GENCODE group processing of GENCODE VM23 (markd)
    # 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/mm10/bed/gencodeVM23
    pushd /hive/data/genomes/mm10/bed/gencodeVM23

    (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/gencodeGenerateTrackDbs mm10 M23 98 'Sept 2019'

    # If being pushed public, update 'Release Notes' in
    # human/mm10/wgEncodeGencodeSuper.html

    # edit human/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeVM23.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM23
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all
    # if pushing public: add ticket and MARK QA READY

2019-08-30: repeat above for final release
    mv /hive/data/genomes/mm10/bed/gencodeVM23 /hive/data/genomes/mm10/bed/gencodeVM23pre
    # redo do above imports

    for t in tables/* ; do cmp ../gencodeVM23pre/$t $t ; done

    Changes:
    wgEncodeGencode2wayConsPseudoVM23.gp 
    wgEncodeGencodeAttrsVM23.tab
    wgEncodeGencodePolyaVM23.gp
    wgEncodeGencodeTagVM23.tab
    only attrs and maybe tags matter to hgGene gencode

    mkdir pre-diffs
    diff ../gencodeVM23pre/tables/wgEncodeGencodeAttrsVM23.tab tables/wgEncodeGencodeAttrsVM23.tab >pre-diffs/wgEncodeGencodeAttrsVM23.diff
    diff ../gencodeVM23pre/tables/wgEncodeGencodeTagVM23.tab tables/wgEncodeGencodeTagVM23.tab >pre-diffs/wgEncodeGencodeTagVM23.diff

    # wgEncodeGencodeAttrsVM23: experimental confirmation level changed on a few pseudogenes
    # wgEncodeGencodeTagVM23: pseudo_consens changed on a few pseudogenes.


##############################################################################
2019-11-16: import of UCSC GENCODE group processing of GENCODE VM24 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/mm10/bed/gencodeVM24
    pushd /hive/data/genomes/mm10/bed/gencodeVM24

    (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/gencodeGenerateTrackDbs mm10 M24 99 'Nov 2019'

    # If being pushed public, update 'Release Notes' in
    # human/mm10/wgEncodeGencodeSuper.html

    # edit human/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeVM24.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM24
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all
    # if pushing public: add ticket and MARK QA READY

##############################################################################
2020-01-16: import of UCSC GENCODE group processing of GENCODE VM24 (markd)
    # deprecate pre-release
    mv /hive/data/genomes/mm10/bed/gencodeVM24 /hive/data/genomes/hg38/bed/gencodeVM24pre
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24
    pushd /hive/data/genomes/mm10/bed/gencodeVM24

    (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/gencodeGenerateTrackDbs mm10 M24 99 'Jan 2020'

    # If being pushed public, update 'Release Notes' in
    # mouse/mm10/wgEncodeGencodeSuper.html

    # edit human/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeVM24.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM24
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=mm10 alpha
    # if pushing public: add ticket and MARK QA READY

##############################################################################
2020-03-11: import of UCSC GENCODE group processing of GENCODE VM25 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/mm10/bed/gencodeVM25Pre
    pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre

    (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/gencodeGenerateTrackDbs mm10 M25 100 'March 2020'

    # Update 'Release Notes'
    # mouse/mm10/wgEncodeGencodeSuper.html

    # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include
    make DBS=mm10

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeVM25.joiner
    # verify with:
    pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=mm10 alpha
    # if pushing public: add ticket and MARK QA READY

###
2020-03-11: final release (markd)
    mkdir -p /hive/data/genomes/mm10/bed/gencodeVM25
  repeat above, only making release month April
    ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M25 100 'April 2020'

