5f313d07411a062ed7d4995781c7c1f464015ad3 markd Thu Oct 17 23:35:14 2024 -0700 import of GENCODE VM36 diff --git src/hg/makeDb/doc/mm39/gencode.txt src/hg/makeDb/doc/mm39/gencode.txt index d06aa2f..7ca8b4e 100644 --- src/hg/makeDb/doc/mm39/gencode.txt +++ src/hg/makeDb/doc/mm39/gencode.txt @@ -478,42 +478,43 @@ # 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 ############################################################################## 2024-07-31: import of UCSC GENCODE group processing of GENCODE VM36 pre-release for GENCODE Versions (markd) +2024-10-17: import of final release # 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' + ensdate='Oct 2024' # edit hg/makeDb/outside/gencode/gencodeLoad.mk to set release and ensembl versions # download, build and load tables mkdir -p /hive/data/genomes/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 ${ver} ${ensver} "${ensdate}"