0f6f8c5cdfc1c5385c814102a4fa59afb08d2849 markd Wed Jul 31 23:45:27 2024 -0700 import of GENCODE v47, v47lift37, and vM36 pre-releases diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt index 4b9c97a..d06aa2f 100644 --- src/hg/makeDb/doc/mm39/gencode.txt +++ src/hg/makeDb/doc/mm39/gencode.txt @@ -1,528 +1,536 @@ ############################################################################## 2021-03-12: import of UCSC GENCODE group processing of GENCODE VM26 (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM26 pushd /hive/data/genomes/mm39/bed/gencodeVM26 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M26 103 'Feb 2021' # If being pushed public, update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM26.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM26 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner Error: 55597 of 140725 elements (39.508%) of mm39.wgEncodeGencodeAttrsVM26.transcriptId are not in key wgEncodeGencodeExonSupportVM26.transcriptId line 5880 of /cluster/home/markd/kent/src/hg/makeDb/schema/all.joiner # however, these are not currently used by the browser, so modify joiner check. Check # with GENCODE is this is expected, might be a cleanup on move to mm39 # check tracks in browser sandbox # commit all make DBS=mm39 alpha # if pushing public: add ticket and MARK QA READY ############################################################################## 2021-06-29: import of UCSC GENCODE group processing of GENCODE VM27 (markd) update from pre-release # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM27 pushd /hive/data/genomes/mm39/bed/gencodeVM27 (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema mm39 M27 104 'May 2021' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM27.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM27 make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # however, these are not currently used by the browser, so modify joiner check. Check # with GENCODE is this is expected, might be a cleanup on move to mm39 # check tracks in browser sandbox # commit all make DBS=mm39 alpha # if pushing public: add ticket and MARK QA READY ############################################################################## 2021-10-15: import of UCSC GENCODE group processing of GENCODE VM28 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M28 105 'Oct 2021' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM28/hgcImportPre.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImportPre make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # however, these are not currently used by the browser, so modify joiner check. Check # with GENCODE is this is expected, might be a cleanup on move to mm39 # check tracks in browser sandbox # commit all make DBS=mm39 alpha # if pushing public: add ticket and MARK QA READY ############################################################################## 2022-01-16: import of UCSC GENCODE group processing of GENCODE VM28 final (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport (time nice make -kO -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M28 105 'Oct 2021' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM28/hgcImport.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM28/hgcImport make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # however, these are not currently used by the browser, so modify joiner check. Check # with GENCODE is this is expected, might be a cleanup on move to mm39 # check tracks in browser sandbox # commit all make DBS=mm39 alpha # add ticket and MARK QA READY ############################################################################## 2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M29 106 'Feb 2022' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM29/hgcImportPre.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImportPre make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all make DBS=mm39 alpha ############################################################################## 2022-01-26: import of UCSC GENCODE group processing of GENCODE VM29 release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M29 106 'Feb 2022' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM29/hgcImport.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM29/hgcImport make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all make DBS=mm39 alpha ############################################################################## 2022-05-13: import of UCSC GENCODE group processing of GENCODE VM30 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M30 107 'June 2022' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include as alpha jkmake DBS=mm39 # edit all.joiner to add ~/tmp/gencodeVM30.joiner pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImportPre make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all make DBS=mm39 alpha ############################################################################## 2022-07-12: import of UCSC GENCODE group processing of GENCODE VM30 release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M30 107 'July 2022' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM30/hgcImport.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM30/hgcImport make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2022-11-03: import of UCSC GENCODE group processing of GENCODE VM31 release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport # get initial version of transcript_rankings, http://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre/Gencode_mouse/release_M31/gencode.vM31.transcript_rankings.txt.gz (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M31 108 'Oct 2022' # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # edit all.joiner to add ~/tmp/gencodeVM31/hgcImport.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM31/hgcImport make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2022-12-29: import of UCSC GENCODE group processing of GENCODE VM32 pre-release (markd) 2023-02-13: import of UCSC GENCODE group processing of GENCODE VM32 final release (markd) pre-release moved to hgcImportPre, notes revised # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM32/hgcImport pushd /hive/data/genomes/mm39/bed/gencodeVM32/hgcImport (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M32 109 'Feb 2023' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit all.joiner to add ~/tmp/gencodeVM32/hgcImport.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM32/hgcImport make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2023-04-25: import of UCSC GENCODE group processing of GENCODE VM33 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions pre="Pre" 2023-04-25: import of UCSC GENCODE group processing of GENCODE VM33 final release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions pre="" # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre} pushd /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre} (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M33 110 'July 2023' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include jkmake DBS=mm39 ## only if being pushed to RR: # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html # edit all.joiner to add ~/tmp/gencodeVM33/hgcImport${pre}.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM33/hgcImport${pre} make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2023-04-25: import of UCSC GENCODE group processing of GENCODE VM34 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # set shell variable: pre="Pre" # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M34 111 'Nov 2023' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include ## only if being pushed to RR: # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html jkmake DBS=mm39 # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2024-01-11: import of UCSC GENCODE group processing of GENCODE VM34 final elease (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # set shell variable: pre="" # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M34 111 'Jan 2024' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include ## only if being pushed to RR: # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html jkmake DBS=mm39 # edit all.joiner to add ~/tmp/gencodeVM34/hgcImport${pre}.joiner # already added for pre-release # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM34/hgcImport${pre} make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## 2024-03-04: import of UCSC GENCODE group processing of GENCODE VM35 pre-release (markd) # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # set shell variable: pre="Pre" # download, build and load tables mkdir -p /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M35 112 'April 2024' # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include ## only if being pushed to RR: # Update 'Release Notes' in # mouse/mm39/wgEncodeGencodeSuper.html jkmake DBS=mm39 # edit all.joiner to add ~/tmp/gencodeVM35/hgcImport${pre}.joiner # already added for pre-release # verify with: pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ############################################################################## -2024-05-14: import of UCSC GENCODE group processing of GENCODE VM35 release (markd) +2024-07-31: import of UCSC GENCODE group processing of GENCODE VM36 pre-release for GENCODE Versions (markd) - # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # set shell variable: + # pre-release shell variables + ver=M36 + ensver=113 + pre="Pre" + ensdate='Sept 2024 pre-release' + # release shell variables + ver=M36 + ensver=113 pre="" + ensdate='Sept 2024' + + # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables - mkdir -p /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} - pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} + mkdir -p /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre} + pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre} (time nice make -j 10 -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk) >&build.1.out& # compare tables from previous release to see if number changed makes # sense. Results are in gencode-cmp.tsv # generate trackDb and joiner blurb pushd ~/kent/src/hg/makeDb/trackDb - ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 M35 112 'May 2024' + ../../makeDb/outside/gencode/bin/gencodeGenerateTrackDbs mm39 ${ver} ${ensver} "${ensdate}" # edit mouse/mm39/trackDb.gencode.ra to add new .ra file include + # edit all.joiner to add ~/tmp/gencodeV${ver}.joiner - ## only if being pushed to RR: - # Update 'Release Notes' in + # if final release, Update 'Release Notes' # mouse/mm39/wgEncodeGencodeSuper.html jkmake DBS=mm39 - # edit all.joiner to add ~/tmp/gencodeVM35/hgcImport${pre}.joiner - # already added for pre-release - # verify with: - pushd /hive/data/genomes/mm39/bed/gencodeVM35/hgcImport${pre} + pushd /hive/data/genomes/mm39/bed/gencodeV${ver}/hgcImport${pre} make -f ~/kent/src/hg/makeDb/outside/gencode/gencodeLoad.mk joinerCheck + # check tracks in browser sandbox # commit all jkmake DBS=mm39 alpha ##############################################################################