7bd8c4f2fd1c56e7bb81ac0235944ab82cfabaea markd Wed Apr 29 13:46:43 2020 -0700 import of GENCODE VM25 diff --git src/hg/makeDb/doc/mm10.gencode.txt src/hg/makeDb/doc/mm10.gencode.txt index 3bef3d8..d391de2 100644 --- src/hg/makeDb/doc/mm10.gencode.txt +++ src/hg/makeDb/doc/mm10.gencode.txt @@ -1,954 +1,960 @@ ############################################################################## 2013-12-13: import of UCSC GENCODE group processing of GENCODE VM2 (markd) mkdir -p /hive/data/genomes/mm10/bed/gencodeVM2 cd /hive/data/genomes/mm10/bed/gencodeVM2 # create Makefile from previous one. cp /hive/data/genomes/hg19/bed/gencodeV19/Makefile . # download, build and load tables (time nice make -j 10) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. # NOT DONE THIS TIME, SINCE THIS is the first mouse. make cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. ## Important to make sure filter attrs.transcriptType matches current set ## figured out with select distinct transcriptType from wgEncodeGencodeAttrsVM2 order by transcriptType; cd kent/src/hg/makeDb/trackDb cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM2.ra cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM2.html # edit these plus human/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM2.ra in reverse order with previous # tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous -0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers ### track handler for this version of gencode: registerTrackHandler("wgEncodeGencodeVM2", gencodeGeneMethods); # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed cd /hive/data/genomes/mm10/bed/gencodeVM2 make joinerCheck # see output in check/joiner.out ############################################################################## # 2014-08-17: import of UCSC GENCODE group processing of GENCODE VM3 (markd) # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM3/data cd /hive/data/genomes/mm10/bed/gencodeVM3 # download gencode release cd data wget -nv -r -np ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3 mv ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M3 . rm -rf ftp.sanger.ac.uk cd .. # create Makefile from previous one. cp /hive/data/genomes/mm10/bed/gencodeVM2/Makefile . # build and load tables (time nice make -j 10) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. ## Important to make sure filter attrs.transcriptType matches current set ## figured out with select distinct transcriptType from wgEncodeGencodeAttrsVM3 order by transcriptType; cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM3.ra cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM3.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM3.ra in reverse order with previous # tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers ### track handler for this version of gencode: registerTrackHandler("wgEncodeGencodeVM3", gencodeGeneMethods); # update all.joiner and validate # look for the last section `begin Gencode VM?' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed cd /hive/data/genomes/mm10/bed/gencodeVM3 make joinerCheck # output in check/joiner.out ############################################################################ # 2014-12-05: import of UCSC GENCODE group processing of GENCODE VM4 (markd) # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM4/data cd /hive/data/genomes/mm10/bed/gencodeVM4 # create Makefile from previous one. # WARNING: next build start with hg/makeDb/outside/gencode/gencodeLoad.mk cp /hive/data/genomes/hg38/bed/gencodeV21/Makefile . # download, build and load tables (time nice make -j 10) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. ## Important to make sure filter attrs.transcriptType matches current set ## figured out with select distinct transcriptType from wgEncodeGencodeAttrsVM4 order by transcriptType; cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM2.ra mouse/mm10/wgEncodeGencodeVM4.ra cp mouse/mm10/wgEncodeGencodeVM2.html mouse/mm10/wgEncodeGencodeVM4.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM4.ra in reverse order with previous # tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. ### IMPORTANT: make sure that hgTracks/gencodeTracks.c registers ### track handler for this version of gencode: registerTrackHandler("wgEncodeGencodeVM4", gencodeGeneMethods); # update all.joiner and validate # look for the last section `begin Gencode VM?' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed cd /hive/data/genomes/mm10/bed/gencodeVM4 make joinerCheck # output in check/joiner.out ######################################################################### 2015-06-29-13: import of UCSC GENCODE group processing of GENCODE VM5 (markd) # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM5 cd /hive/data/genomes/mm10/bed/gencodeVM5 # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set # release and transcript support versions # download, build and load tables (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. ## Important to make sure filter attrs.transcriptType matches current set ## figured out with select distinct transcriptType from wgEncodeGencodeAttrsVM5 order by transcriptType; cd kent/src/hg/makeDb/trackDb cp human/mm10/wgEncodeGencodeV18.ra human/mm10/wgEncodeGencodeVM5.ra cp human/mm10/wgEncodeGencodeV18.html human/mm10/wgEncodeGencodeVM5.html # edit these plus human/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM5.ra in reverse order with previous # tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM5 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2015-10-02: import of UCSC GENCODE group processing of GENCODE VM7 (markd) # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM7 cd /hive/data/genomes/mm10/bed/gencodeVM7 # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set # release and transcript support versions # download, build and load tables (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructiuons in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM4.ra mouse/mm10/wgEncodeGencodeVM7.ra cp mouse/mm10/wgEncodeGencodeVM4.html mouse/mm10/wgEncodeGencodeVM7.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM7.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM7 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2016-03-14: import of UCSC GENCODE group processing of GENCODE VM8 (markd) # not to be pushed to RR # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM8 cd /hive/data/genomes/mm10/bed/gencodeVM8 # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructions in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM7.ra mouse/mm10/wgEncodeGencodeVM8.ra cp mouse/mm10/wgEncodeGencodeVM7.html mouse/mm10/wgEncodeGencodeVM8.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM8.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM8 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2016-03-14: import of UCSC GENCODE group processing of GENCODE VM9 (markd) # download files mkdir -p /hive/data/genomes/mm10/bed/gencodeVM9 cd /hive/data/genomes/mm10/bed/gencodeVM9 # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructions in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM9.ra cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM9.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM9.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM9 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2016-07-22: import of UCSC GENCODE group processing of GENCODE VM10 (markd) # will not be pushed to the RR. # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM10 pushd /hive/data/genomes/mm10/bed/gencodeVM10 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructions in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM9.ra mouse/mm10/wgEncodeGencodeVM10.ra cp mouse/mm10/wgEncodeGencodeVM9.html mouse/mm10/wgEncodeGencodeVM10.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM10.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. [ONLY if it's going to be pushed] # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM10 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2016-10-27: import of UCSC GENCODE group processing of GENCODE VM11 (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM11 cd /hive/data/genomes/mm10/bed/gencodeVM11 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk cmpRelease >gencode-cmp.tsv ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructions in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM8.ra mouse/mm10/wgEncodeGencodeVM11.ra cp mouse/mm10/wgEncodeGencodeVM8.html mouse/mm10/wgEncodeGencodeVM11.html # edit these plus mouse/mm10/trackDb.wgEncode.ra # - set priorities in wgEncodeGencodeVM11.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM11 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ############################################################################## 2016-12-08: import of UCSC GENCODE group processing of GENCODE VM12 (markd) No being pushed to RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM12 cd /hive/data/genomes/mm10/bed/gencodeVM12 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv- check to see if sizes make sense ## Copy and update trackDb files from previous release. ## Change version and use lower priority so it sorts to top of ## super track page. Follow instructions in ra file to ensure ## filters are correct. cd kent/src/hg/makeDb/trackDb cp mouse/mm10/wgEncodeGencodeVM11.ra mouse/mm10/wgEncodeGencodeVM12.ra cp mouse/mm10/wgEncodeGencodeVM11.html mouse/mm10/wgEncodeGencodeVM12.html # edit these plus mouse/mm10/trackDb.ra # - set priorities in wgEncodeGencodeVM12.ra tracks so newest shows up first # priority - set to previous version priority minus 0.001 # searchPriority - set each to previous minus 0.001 # - make current track default to pack and hide previous [ONLY if it's going to be pushed] # superTrack wgEncodeGencodeSuper pack # - Update wgEncodeGencodeSuper.html to describe new release and to # pick up other updates. # DID NOT UPDATE all.joiner SINCE NOT BEING PUSHED PUBLIC # update all.joiner and validate # look for the last section `begin Gencode V??' in all.joiner # and copy and update version # repeat this until happy, editing minCheck as needed # output in check/joiner.out cd /hive/data/genomes/mm10/bed/gencodeVM12 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck ######################################################################### 2017-04-16: import of UCSC GENCODE group processing of GENCODE VM13 (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM13 pushd /hive/data/genomes/mm10/bed/gencodeVM13 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M13 88 'March 2017' # edit mouse/mm10/trackDb.ra to add new .ra file include make DBS=mm10 # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' # to describe new release. [ONLY if it's going to be pushed] # edit all.joiner to add ~/tmp/gencodeVM13.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM13 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all ############################################################################## 2017-05-31: import of UCSC GENCODE group processing of GENCODE VM14 (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM14 pushd /hive/data/genomes/mm10/bed/gencodeVM14 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M14 89 'May 2017' # edit mouse/mm10/trackDb.wgEncode.ra to add new .ra file include make DBS=mm10 # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' # to describe new release. [ONLY if it's going to be pushed] # edit all.joiner to add ~/tmp/gencodeVM14.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM14 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all ############################################################################## 2017-09-15: import of UCSC GENCODE group processing of GENCODE VM15 (markd) # not to push to the RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM15 pushd /hive/data/genomes/mm10/bed/gencodeVM15 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M15 90 'Aug 2017' # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' # to describe new release. [ONLY if it's going to be pushed] # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM15.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM15 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all ############################################################################## 2017-12-17: import of UCSC GENCODE group processing of GENCODE VM16 (markd) # being push to the RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM16 pushd /hive/data/genomes/mm10/bed/gencodeVM16 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017' # Update mouse/mm10/wgEncodeGencodeSuper.html and update 'Release Notes' # to describe new release. [ONLY if it's going to be pushed] # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM16.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM16 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. ######################################################################### 2018-03-08: update UCSC GENCODE VM16 to include protein id (for VAI) and fix PAR tag cd /hive/data/genomes/mm10/bed/gencodeVM16 # save existing data mkdir -p prev/pre-proteinId mv tables/wgEncodeGencodeAttrsVM16.tab tables/wgEncodeGencodeTagVM16.tab prev/pre-proteinId/ mv loaded/wgEncodeGencodeAttrsVM16.tab.loaded loaded/wgEncodeGencodeTagVM16.tab.loaded prev/pre-proteinId/ mv data/gencode.tsv prev/pre-proteinId/ cp -p data/gencode.vM16.transcriptionSupportLevel.tab prev/pre-proteinId/ # edit gencodeLoad.mk to set mm10 as target # get gencode.tsv without rebuild TSL file or loading tables that don't change ~markd/compbio/ccds/ccds2/output/bin/x86_64/opt/gencodeGxfToAttrs --keepGoing data/release_M16/gencode.vM16.chr_patch_hapl_scaff.annotation.gtf.gz data/gencode.tsv make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk loaded/wgEncodeGencodeAttrsVM16.tab.loaded loaded/wgEncodeGencodeTagVM16.tab.loaded # 2018-03-19: update search to include protein id cd kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M16 91 'Dec 2017' ######################################################################### 2018-07-01: import of UCSC GENCODE group processing of GENCODE VM17 (markd) # not being push to the RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM17 pushd /hive/data/genomes/mm10/bed/gencodeVM17 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M17 92 'Mar 2018' ## only if being pushed to RR: # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM17.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM17 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. ############################################################################## 2018-08-03: import of UCSC GENCODE group processing of GENCODE VM18 (markd) # being push to the RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM18 pushd /hive/data/genomes/mm10/bed/gencodeVM18 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M18 93 'July 2018' ## only if being pushed to RR: # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM18.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM18 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=mm10 ######################################################################### 2018-11-10: import of UCSC GENCODE group processing of GENCODE VM19 (markd) # not being push to the RR # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM19 pushd /hive/data/genomes/mm10/bed/gencodeVM19 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M19 94 'Oct 2018' ## only if being pushed to RR: (skipped) # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: (SKIPPED) # edit all.joiner to add ~/tmp/gencodeVM19.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM19 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=mm10 ############################################################################## 2018-11-30: import of UCSC GENCODE group processing of GENCODE VM20 prerelease (markd) # This is a prerelease for testing and is *not* to pushed until the final release. # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM20 pushd /hive/data/genomes/mm10/bed/gencodeVM20 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M20 95 'Dec 2018' ## only if being pushed to RR: (skipped) # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: (SKIPPED) # edit all.joiner to add ~/tmp/gencodeVM20.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM20 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=mm10 ############################################################################## 2019-04-08: import of UCSC GENCODE group processing of GENCODE VM20 (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM21 pushd /hive/data/genomes/mm10/bed/gencodeVM21 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M21 96 'Apr 2019' ## only if being pushed to RR: # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM21.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM21 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=mm10 # commit all # if pushing public, add ticket and MARK QA READY ######################################################################### 2019-07-03: import of UCSC GENCODE group processing of GENCODE VM22 (markd) # Replaced import of pre-release # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM22 pushd /hive/data/genomes/mm10/bed/gencodeVM22 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& ## gencode-cmp.tsv check to see if sizes make sense # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M22 97 'June 2019' ## only if being pushed to RR: # Update mouse/mm10/wgEncodeGencodeSuper.html # Update 'Release Notes' to describe new release. # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM22.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM22 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck db=mm10 # commit all and make push request, the file tables.lst will have the # list of tables for the push request. cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=mm10 # commit all # if pushing public, add ticket and MARK QA READY ############################################################################## 2019-08-30: import of UCSC GENCODE group processing of GENCODE VM23 (markd) # PRE-RELEASE # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM23 pushd /hive/data/genomes/mm10/bed/gencodeVM23 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M23 98 'Sept 2019' # If being pushed public, update 'Release Notes' in # human/mm10/wgEncodeGencodeSuper.html # edit human/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM23.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM23 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # commit all # if pushing public: add ticket and MARK QA READY 2019-08-30: repeat above for final release mv /hive/data/genomes/mm10/bed/gencodeVM23 /hive/data/genomes/mm10/bed/gencodeVM23pre # redo do above imports for t in tables/* ; do cmp ../gencodeVM23pre/$t $t ; done Changes: wgEncodeGencode2wayConsPseudoVM23.gp wgEncodeGencodeAttrsVM23.tab wgEncodeGencodePolyaVM23.gp wgEncodeGencodeTagVM23.tab only attrs and maybe tags matter to hgGene gencode mkdir pre-diffs diff ../gencodeVM23pre/tables/wgEncodeGencodeAttrsVM23.tab tables/wgEncodeGencodeAttrsVM23.tab >pre-diffs/wgEncodeGencodeAttrsVM23.diff diff ../gencodeVM23pre/tables/wgEncodeGencodeTagVM23.tab tables/wgEncodeGencodeTagVM23.tab >pre-diffs/wgEncodeGencodeTagVM23.diff # wgEncodeGencodeAttrsVM23: experimental confirmation level changed on a few pseudogenes # wgEncodeGencodeTagVM23: pseudo_consens changed on a few pseudogenes. ############################################################################## 2019-11-16: import of UCSC GENCODE group processing of GENCODE VM24 PRE-RELEASE (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24 pushd /hive/data/genomes/mm10/bed/gencodeVM24 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M24 99 'Nov 2019' # If being pushed public, update 'Release Notes' in # human/mm10/wgEncodeGencodeSuper.html # edit human/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM24.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM24 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # commit all # if pushing public: add ticket and MARK QA READY ############################################################################## 2020-01-16: import of UCSC GENCODE group processing of GENCODE VM24 (markd) # deprecate pre-release mv /hive/data/genomes/mm10/bed/gencodeVM24 /hive/data/genomes/hg38/bed/gencodeVM24pre # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM24 pushd /hive/data/genomes/mm10/bed/gencodeVM24 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M24 99 'Jan 2020' # If being pushed public, update 'Release Notes' in # mouse/mm10/wgEncodeGencodeSuper.html # edit human/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM24.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM24 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all make DBS=mm10 alpha # if pushing public: add ticket and MARK QA READY ############################################################################## 2020-03-11: import of UCSC GENCODE group processing of GENCODE VM25 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm10/bed/gencodeVM25Pre pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M25 100 'March 2020' - # If being pushed public, update 'Release Notes' if pushing puyblic. + # Update 'Release Notes' # mouse/mm10/wgEncodeGencodeSuper.html # edit mouse/mm10/trackDb.gencode.ra to add new .ra file include make DBS=mm10 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM25.joiner # verify with: pushd /hive/data/genomes/mm10/bed/gencodeVM25Pre make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all make DBS=mm10 alpha # if pushing public: add ticket and MARK QA READY +### +2020-03-11: final release (markd) + mkdir -p /hive/data/genomes/mm10/bed/gencodeVM25 + repeat above, only making release month April + ../../makeDb/outside/gencode/gencodeGenerateTrackDbs mm10 M25 100 'April 2020' +