#########################################################################
2014-08-11: import of UCSC GENCODE group processing of GENCODE V20 (markd)
    # download files
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV20/data
    cd /hive/data/genomes/hg38/bed/gencodeV20

    # download gencode release
    cd data
    wget -nv -r -np ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_20
    mv ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_20 .
    rm -rf ftp.sanger.ac.uk

    cd ..
    # create Makefile from previous one.
    cp /hive/data/genomes/hg19/bed/gencodeV19/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 wgEncodeGencodeAttrsV20 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/hg38/wgEncodeGencodeV18.ra human/hg38/wgEncodeGencodeV20.ra
    cp human/hg38/wgEncodeGencodeV18.html human/hg38/wgEncodeGencodeV20.html

    # edit these plus human/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV20.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("wgEncodeGencodeV20", 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/hg38/bed/gencodeV20
    make joinerCheck  # output in check/joiner.out


#########################################################################
2014-10-16: import of UCSC GENCODE group processing of GENCODE V21 (markd)
    # download files
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV21/data
    cd /hive/data/genomes/hg38/bed/gencodeV21

    # create Makefile from previous one.
    # WARNING: next build start with hg/makeDb/outside/gencode/gencodeLoad.mk
    cp /hive/data/genomes/hg38/bed/gencodeV20/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 wgEncodeGencodeAttrsV21 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/hg38/wgEncodeGencodeV18.ra human/hg38/wgEncodeGencodeV21.ra
    cp human/hg38/wgEncodeGencodeV18.html human/hg38/wgEncodeGencodeV21.html

    # edit these plus human/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV21.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("wgEncodeGencodeV21", 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/hg38/bed/gencodeV21
    make joinerCheck  # output in check/joiner.out


#########################################################################
2015-03-13: import of UCSC GENCODE group processing of GENCODE V22 (markd)
    # download files
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV22
    cd /hive/data/genomes/hg38/bed/gencodeV22

    # 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 wgEncodeGencodeAttrsV22 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/hg38/wgEncodeGencodeV18.ra human/hg38/wgEncodeGencodeV22.ra
    cp human/hg38/wgEncodeGencodeV18.html human/hg38/wgEncodeGencodeV22.html

    # edit these plus human/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV22.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/hg38/bed/gencodeV22
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2015-10-02: import of UCSC GENCODE group processing of GENCODE V23 (markd)
    # download files
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV23
    cd /hive/data/genomes/hg38/bed/gencodeV23

    # 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 wgEncodeGencodeAttrsV23 order by transcriptType;
    cd kent/src/hg/makeDb/trackDb
    cp human/hg38/wgEncodeGencodeV22.ra human/hg38/wgEncodeGencodeV23.ra
    cp human/hg38/wgEncodeGencodeV22.html human/hg38/wgEncodeGencodeV23.html

    # edit these plus human/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV23.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/hg38/bed/gencodeV23
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2015-12-08: import of UCSC GENCODE group processing of GENCODE V24 (markd)
    # download files
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV24
    cd /hive/data/genomes/hg38/bed/gencodeV24

    # 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 (results in gencode-cmp.tsv)
        make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease

    ## 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 human/hg38/wgEncodeGencodeV23.ra human/hg38/wgEncodeGencodeV24.ra
    cp human/hg38/wgEncodeGencodeV23.html human/hg38/wgEncodeGencodeV24.html


    # edit these plus human/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV24.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
    ### NOT DONE SINCE TRACK NOT BEING PUSHED
    cd /hive/data/genomes/hg38/bed/gencodeV24
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2016-07-23: import of UCSC GENCODE group processing of GENCODE V25 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV25
    pushd /hive/data/genomes/hg38/bed/gencodeV25
    (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/hg38/wgEncodeGencodeVM9.ra mouse/hg38/wgEncodeGencodeV25.ra
    cp mouse/hg38/wgEncodeGencodeVM9.html mouse/hg38/wgEncodeGencodeV25.html

    # edit these plus mouse/hg38/trackDb.wgEncode.ra
    # - set priorities in wgEncodeGencodeV25.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/hg38/bed/gencodeV25
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

#########################################################################
2017-04-16: import of UCSC GENCODE group processing of GENCODE V26 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV26
    pushd /hive/data/genomes/hg38/bed/gencodeV26
    (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 hg38 26 88 'March 2017'

    # edit human/hg38/trackDb.wgEncode.ra to add new .ra file include
    make DBS=hg38

    # Update human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit  all.joiner to add ~/tmp/gencodeV26.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV26
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all
#########################################################################
2017-09-14: import of UCSC GENCODE group processing of GENCODE V27 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV27
    pushd /hive/data/genomes/hg38/bed/gencodeV27
    (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 hg38 27 90 'Aug 2017'

    # Update human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.wgEncode.ra to add new .ra file include
    make DBS=hg38

    # edit  all.joiner to add ~/tmp/gencodeV27.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV27
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2018-03-07: update UCSC GENCODE V27 to include protein id (for VAI) and fix PAR tag

# save existing data, move a
mkdir -p prev/pre-proteinId
mv data/gencode.tab prev/pre-proteinId/
mv tables/wgEncodeGencodeAttrsV27.tab tables/wgEncodeGencodeTagV27.tab prev/pre-proteinId/
mv loaded/wgEncodeGencodeAttrsV27.tab.loaded loaded/wgEncodeGencodeTagV27.tab.loaded prev/pre-proteinId/

# rebuild, getting protein ids.
make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk loadTables >&prot-ids.log

# 2018-03-19: update search to include protein id
cd kent/src/hg/makeDb/trackDb
../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg38 27 90 'Aug 2017'

#########################################################################
2018-04-11: import of UCSC GENCODE group processing of GENCODE V28 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV28
    pushd /hive/data/genomes/hg38/bed/gencodeV28
    (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 hg38 28 92 'Apr 2018'

    # Update human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.wgEncode.ra to add new .ra file include
    make DBS=hg38

    # edit  all.joiner to add ~/tmp/gencodeV28.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV28
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2018-09-05: import of UCSC GENCODE group processing of GENCODE V29 (markd)
    2018-11-09 this was the prerelease and the /hive/data/genomes/hg38/bed/gencodeV29
    was renamed to /hive/data/genomes/hg38/bed/gencodeV29.pre when the full release was
    downloaded.
    
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # This is a pre-release from
    # ftp://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_human/release_29/

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV29
    pushd /hive/data/genomes/hg38/bed/gencodeV29

    # pre-release contained invalid biotype, fix for now
    mv gencode.v29.chr_patch_hapl_scaff.annotation.gtf.gz  gencode.v29.chr_patch_hapl_scaff.annotation.orig.gtf.gz 
    zcat gencode.v29.chr_patch_hapl_scaff.annotation.orig.gtf.gz | sed -e 's/"lincrna"/"lincRNA"/g' | gzip -c>  gencode.v29.chr_patch_hapl_scaff.annotation.gtf.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/gencodeGenerateTrackDbs hg38 29 94 'Sept 2018'

    # Edit human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.wgEncode.ra to add new .ra file include
    make DBS=hg38

    # edit  all.joiner to add ~/tmp/gencodeV29.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV29
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2018-11-09: import of UCSC GENCODE group processing of GENCODE V29 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV29
    pushd /hive/data/genomes/hg38/bed/gencodeV29

    (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 hg38 29 94 'Oct 2018'

    # Edit human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.wgEncode.ra to add new .ra file include
    make DBS=hg38

    # edit  all.joiner to add ~/tmp/gencodeV29.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV29
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2019-04-08: import of UCSC GENCODE group processing of GENCODE V30 (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV30
    pushd /hive/data/genomes/hg38/bed/gencodeV30

    (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 hg38 30 96 'Apr 2019'

    # Edit human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeV30.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV30
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2019-07-03: import of UCSC GENCODE group processing of GENCODE V31 (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/hg38/bed/gencodeV31a
    pushd /hive/data/genomes/hg38/bed/gencodeV31

    (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 hg38 31 97 'June 2019'

    # Edit human/hg38/wgEncodeGencodeSuper.html and update 'Release Notes'
    # to describe new release. [ONLY if it's going to be pushed]

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeV31.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV31
    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: import of UCSC GENCODE group processing of GENCODE V32 (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/hg38/bed/gencodeV32
    pushd /hive/data/genomes/hg38/bed/gencodeV32

    (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 hg38 32 98 'Sept 2019'

    # If being pushed public, update 'Release Notes' in
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeV32.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV32
    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/hg38/bed/gencodeV32 /hive/data/genomes/hg38/bed/gencodeV32pre
    # redo do above imports

    for t in tables/* ; do cmp ../gencodeV32pre/$t $t ; done

    Changes:
    wgEncodeGencode2wayConsPseudoV32.gp 
    wgEncodeGencodeAttrsV32.tab
    wgEncodeGencodePolyaV32.gp
    wgEncodeGencodeTagV32.tab
    only attrs and maybe tags matter to hgGene gencode

    mkdir pre-diffs
    diff ../gencodeV32pre/tables/wgEncodeGencodeAttrsV32.tab tables/wgEncodeGencodeAttrsV32.tab >pre-diffs/wgEncodeGencodeAttrsV32.diff
    diff ../gencodeV32pre/tables/wgEncodeGencodeTagV32.tab tables/wgEncodeGencodeTagV32.tab >pre-diffs/wgEncodeGencodeTagV32.diff

    # wgEncodeGencodeAttrsV32: experimental conformation level changed on a few pseudogenes
    # wgEncodeGencodeTagV32: pseudo_consens changed on a few pseudogenes.

#########################################################################
2019-11-15: import of UCSC GENCODE group processing of GENCODE V33 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/hg38/bed/gencodeV33
    pushd /hive/data/genomes/hg38/bed/gencodeV33

    (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 hg38 33 99 'Nov 2019'

    # If being pushed public, update 'Release Notes' in
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR:
    # edit all.joiner to add ~/tmp/gencodeV33.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV33
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # commit all

#########################################################################
2020-01-16: import of UCSC GENCODE group processing of GENCODE V33  (markd)
    # deprecate pre-release
    mv /hive/data/genomes/hg38/bed/gencodeV33 /hive/data/genomes/hg38/bed/gencodeV33pre

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV33
    pushd /hive/data/genomes/hg38/bed/gencodeV33

    (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 hg38 33 99 'Jan 2020'

    # Update 'Release Notes' in
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV33.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV33
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY

#########################################################################
2020-03-11: import of UCSC GENCODE group processing of GENCODE V34 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/hg38/bed/gencodeV34Pre
    pushd /hive/data/genomes/hg38/bed/gencodeV34Pre

    (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 hg38 34 100 'Mar 2020'

    # Update 'Release Notes' in if pushing public
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV34.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV34Pre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY

###
2020-04-29 final release markd
  mkdir -p /hive/data/genomes/hg38/bed/gencodeV34

  repeat above, only making release month April
  ../../makeDb/outside/gencode/gencodeGenerateTrackDbs hg38 34 100 'April 2020'

#########################################################################
2020-06-05: import of UCSC GENCODE group processing of GENCODE V35 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/hg38/bed/gencodeV35Pre
    pushd /hive/data/genomes/hg38/bed/gencodeV35Pre

    (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 hg38 35 101 'June 2020'

    # Update 'Release Notes' in if pushing public
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV35.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV35Pre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY
#########################################################################
2020-11-30: import of UCSC GENCODE group GENCODE V36 pre-release  (markd)
    
    # edit hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV36/importi
    pushd /hive/data/genomes/hg38/bed/gencodeV36/import

    (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.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 hg38 36 102 'November 2020'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV36.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV36
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    # SKIP FOR NOW, hgc needs to handle these for testing on hgwdev
    # make DBS=hg38 alpha
#########################################################################
2020-12-19: import of UCSC GENCODE group processing of GENCODE V35 for hgc all gencode  (markd)
    # due to delays in hgGene work, create hgc version
    
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV35/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV35/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
    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 35 101 'Aug 2020'

    # Update 'Release Notes' in if pushing public
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV35.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV35/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY
#########################################################################
2020-12-20: import of UCSC GENCODE group processing of GENCODE V36 for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV36/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV36/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
    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 36 102 'Nov 2020'

    # Update 'Release Notes' in if pushing public
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    make DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV36.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV36/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    make DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY
#########################################################################
2021-03-08: import of UCSC GENCODE group processing of GENCODE V37 for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV37/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV37/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
    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 37 103 'Feb 2021'

    # Update 'Release Notes'
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    ## only if being pushed to RR (may be there from pre-release)
    # edit all.joiner to add ~/tmp/gencodeV37.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV37/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY
#########################################################################
2021-06-28: import of UCSC GENCODE group processing of GENCODE V38 for hgc all gencode  (markd)
    # replace pre-release from 2021-04-06
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV38/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV38/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
    ../outside/gencode/bin/gencodeGenerateTrackDbsOldSchema hg38 38 104 'May 2021'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV38.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV38/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY

2021-09-25:
    It was discovered that most of the alt/patch sequence were missing
    this was due switching over to use the ensemblToUcsc table to map
    GENCODE chromosome names for mm39 pre-release.  The code was modified
    to use the assembly report to make the chromosome names and the
    track rebuilt.
    
#########################################################################
2021-10-13: import of UCSC GENCODE group processing of GENCODE V39 for hgc all gencode  (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/hg38/bed/gencodeV39/hgcImportPre
    pushd /hive/data/genomes/hg38/bed/gencodeV39/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
    ../outside/gencode/bin/gencodeGenerateTrackDbs  hg38 39 105 'Oct 2021'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV39.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV39/hgcImportPre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY

#########################################################################
2022-01-13: import of UCSC GENCODE group processing of GENCODE V39 for hgc all gencode  (markd)
    # 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/hg38/bed/gencodeV39/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV39/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
    ../outside/gencode/bin/gencodeGenerateTrackDbs  hg38 39 105 'Oct 2021'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV39.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV39/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
    # if pushing public: create ticket and MARK QA READY


#########################################################################
2022-01-25: import of UCSC GENCODE group processing of GENCODE V40 pre-release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV40/hgcImportPre
    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImportPre

    (time nice make -O -j 32 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    # reported stray space in
    release_40/gencode.v40.metadata.Pubmed_id.gz

    # 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  hg38 40 106 'Feb 2022'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV40.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImportPre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
#########################################################################
2022-04-21: import of UCSC GENCODE group processing of GENCODE V40 release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV40/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImport

    (time nice make -O -j 32 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out&

    # reported stray space in
    release_40/gencode.v40.metadata.Pubmed_id.gz

    # compare tables from previous release to see if number changed makes
    diff -qr ../hgcImportPre/tables tables
    Files ../hgcImportPre/tables/wgEncodeGencodeAttrsV40.tab and tables/wgEncodeGencodeAttrsV40.tab differ
    Files ../hgcImportPre/tables/wgEncodeGencodeTagV40.tab and tables/wgEncodeGencodeTagV40.tab differ
    cmp <(sort ../hgcImportPre/tables/wgEncodeGencodeAttrsV40.tab) <(sort tables/wgEncodeGencodeAttrsV40.tab)
    cmp <(sort ../hgcImportPre/tables/wgEncodeGencodeTagV40.tab) <(sort tables/wgEncodeGencodeTagV40.tab)
    # Due to sorting differences; code has already been change to sort these for the future

    # 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  hg38 40 106 'Feb 2022'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    jkmake DBS=hg38

    # edit all.joiner to add ~/tmp/gencodeV40.joiner
    # verify with:
    pushd /hive/data/genomes/hg38/bed/gencodeV40/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
#########################################################################
2022-05-13: import of UCSC GENCODE group processing of GENCODE V41 pre-release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV41/hgcImportPre
    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImportPre

    (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 hg38 41 107 'June 2022'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include as alpha

    # edit all.joiner to add ~/tmp/gencodeV41.joiner

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImportPre
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2022-07-12: import of UCSC GENCODE group processing of GENCODE V41 final release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV41/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImport

    (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 hg38 41 107 'July 2022'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to remove alpha

    # edit all.joiner to add ~/tmp/gencodeV41.joiner

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV41/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2022-08-21: import of UCSC GENCODE group processing of GENCODE V42 pre release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV42Pre/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV42Pre/hgcImport

    (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 hg38 42 108 'Sept 2022'

    # add to human/hg38/trackDb.gencode.ra

    # edit all.joiner to add ~/tmp/gencodeV42.joiner

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV42Pre/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2022-10-28: import of UCSC GENCODE group processing of GENCODE V42 final release for hgc all gencode  (markd)
    # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV42/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV42/hgcImport

    # get initial version of transcript_rankings,
    # http://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_human/release_42/gencode.v42.transcript_rankings.txt.gz
    
    (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 hg38 42 108 'Oct 2022'

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to remove alpha

    # edit all.joiner to add ~/tmp/gencodeV42.joiner

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV42/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2022-12-27: import of UCSC GENCODE group processing of GENCODE V43 pre-release for hgc all gencode  (markd)
2023-02-13: import of UCSC GENCODE group processing of GENCODE V43 release for hgc all gencode  (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/hg38/bed/gencodeV43/hgcImport
    pushd /hive/data/genomes/hg38/bed/gencodeV43/hgcImport

    (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 hg38 43 109 'Feb 2023'

    # edit all.joiner to add ~/tmp/gencodeV43.joiner

    # Update 'Release Notes' (for final)
    # human/hg38/wgEncodeGencodeSuper.html

    # edit human/hg38/trackDb.gencode.ra to remove alpha
    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV43/hgcImport
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2023-04-25: import of UCSC GENCODE group processing of GENCODE V44 pre-release for GENCODE Versions (markd)

   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
    pre="Pre"
    [same as below]

2023-07-18: import of UCSC GENCODE group processing of GENCODE V44 pre-release for GENCODE Versions (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/hg38/bed/gencodeV44/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV44/hgcImport${pre}

    (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 hg38 44 110 'July 2023' 

    # edit all.joiner to add ~/tmp/gencodeV44.joiner

    # Update 'Release Notes' (for final, not pre)
    # human/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV44/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2023-10-10: import of UCSC GENCODE group processing of GENCODE V45 pre-release for GENCODE Versions (markd)

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

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}

    (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 hg38 45 111 'Nov 2023'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV45.joiner

    # Update 'Release Notes' (for final, not pre)
    # human/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2024-01-11: import of UCSC GENCODE group processing of GENCODE V45 pre-release for GENCODE Versions (markd)

   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
   # set shell variable:
    pre=""
    [as used below]

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}

    (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 hg38 45 111 'Jan 2024'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include (already done on pre-release)
    # edit all.joiner to add ~/tmp/gencodeV45.joiner

    # Update 'Release Notes' (for final, not pre)
    # human/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV45/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

#########################################################################
2024-03-04: import of UCSC GENCODE group processing of GENCODE V46 pre-release for GENCODE Versions (markd)

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

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}

    (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 hg38 46 112 'April 2024'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV46.joiner

    # Update 'Release Notes' (for final, not pre)
    # human/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha

2024-03-27: re-import track to pick up GENCODE_Primary tag
#########################################################################
2024-05-13: import of UCSC GENCODE group processing of GENCODE V46 release for GENCODE Versions (markd)

   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions
   # set shell variable:
    pre=""
    [as used below]

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

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}

    (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 hg38 46 112 'May 2024'

    # edit human/hg38/trackDb.gencode.ra to add new .ra file include
    # edit all.joiner to add ~/tmp/gencodeV46.joiner

    # Update 'Release Notes' (for final, not pre)
    # human/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/bed/gencodeV46/hgcImport${pre}
    make  -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck

    # check tracks in browser sandbox
    # commit all
    jkmake DBS=hg38 alpha
#########################################################################
2024-07-31: import of UCSC GENCODE group processing of GENCODE V47 pre-release for GENCODE Versions (markd)
2024-10-17: release of GENCODE V47
   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release type and versions

   # pre-release shell variables 
       ver=47
       ensver=113
       pre="Pre"
       ensdate='Sept 2024 pre-release' 
   # release shell variables 
       ver=47
       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/hg38/bed/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV${ver}/hgcImport${pre}

    (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 hg38 ${ver} ${ensver} "${ensdate}"

    # edit human/hg38/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/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/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=hg38 alpha
#########################################################################
2025-02-05: import of UCSC GENCODE group processing of GENCODE V48 pre-release for GENCODE Versions (markd)
2025-05-31: final release
   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release type and versions

   # pre-release shell variables 
       ver=48
       ensver=114
       pre="Pre"
       ensdate='Feb 2025 pre-release' 
   # release shell variables 
       ver=48
       ensver=114
       pre=""
       ensdate='May 2025'
    

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV${ver}/hgcImport${pre}

    (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 hg38 ${ver} ${ensver} "${ensdate}"

    # edit human/hg38/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/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/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=hg38 alpha
#########################################################################
2025-07-28: import of UCSC GENCODE group processing of GENCODE V49 pre-release for GENCODE Versions (markd)
2025-09-08: final release
   # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release type and versions

   # pre-release shell variables 
       ver=49
       ensver=115
       pre="Pre"
       ensdate='July 2025 pre-release' 
   # release shell variables 
       ver=49
       ensver=115
       pre=""
       ensdate='Sept 2025'
    

    # download, build and load tables
    mkdir -p /hive/data/genomes/hg38/bed/gencodeV${ver}/hgcImport${pre}
    pushd /hive/data/genomes/hg38/bed/gencodeV${ver}/hgcImport${pre}

    (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 hg38 ${ver} ${ensver} "${ensdate}"

    # edit human/hg38/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/hg38/wgEncodeGencodeSuper.html

    jkmake DBS=hg38

    # check joiner 
    pushd /hive/data/genomes/hg38/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=hg38 alpha
#########################################################################
