b4cb35b2a3919b84f30a88b41e4a78277528c710 markd Thu Mar 11 15:24:33 2021 -0800 import of GENCODE V37 diff --git src/hg/makeDb/doc/hg38/gencode.txt src/hg/makeDb/doc/hg38/gencode.txt index 0e05a33..3d7cad7 100644 --- src/hg/makeDb/doc/hg38/gencode.txt +++ src/hg/makeDb/doc/hg38/gencode.txt @@ -1,807 +1,840 @@ ######################################################################### 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 +#########################################################################