f804309aff2c2d12b78fc09dc656376e69e75d2c markd Mon Jun 24 14:15:29 2019 -0700 added test case for single block bed and make test file name less silly diff --git src/hg/makeDb/doc/transMapTracks.txt src/hg/makeDb/doc/transMapTracks.txt index 5a37e5c..2499dd7 100644 --- src/hg/makeDb/doc/transMapTracks.txt +++ src/hg/makeDb/doc/transMapTracks.txt @@ -99,31 +99,31 @@ ############################################################################################## # TransMap V5 tracks (2019-06-10 markd) ## - Build code is here: /cluster/home/markd/compbio/repos/git/transMap.git which also requires /cluster/home/markd/compbio/repos/git/pycbio.git git@github.com:diekhans/pipettor.git - Build process: # IMPORTANT: SET VERSION IN transMap-dev/etc/transMapBuildConf.py tmdir=~/compbio/projs/transMap/transMap-dev mkdir -p /hive/data/inside/transMap/V5/logs pushd /hive/data/inside/transMap/V5 - (time nice ${tmdir}/bin/luigiTransMap --workers=32 --logConfFile=${tmdir}/etc/logging.conf ${tmdir}/etc/transMapBuildConf.py) >&logs/2019-06-10.log & + (time nice ${tmdir}/bin/luigiTransMap --workers=64 --logConfFile=${tmdir}/etc/logging.conf ${tmdir}/etc/transMapBuildConf.py) >&logs/2019-06-24.log & # takes maybe 10-14 hours, at the end, check for parasol jobs # that are lost (using one or two stranglers for a few batches), then do para stop -batch=/the/batch/name para push -batch=/the/batch/name # now wait for luigiTransMap to complete. Must manually check log, as # current luigi doesn't exit non-zero if there were errors # create symlinks to /gbdb for bigPsl files ${tmdir}/bin/linkToGbdb ${tmdir}/etc/transMapBuildConf.py # add trackDb entries at top level by editing: src/hg/makeDb/trackDb/trackDb.transMap.ra # create push lists for databases and gbdb files for genomes on hgwbeta: ${tmdir}/bin/mkPushList ${tmdir}/etc/transMapBuildConf.py db.push.lst gbdb.push.lst