371a636b6cf6c5c48f41be953541a62eea58db84 hiram Wed Dec 1 11:31:37 2021 -0800 grcIncident seems to be working OK refs #28331 diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab index c14bccb..52f6ea1 100644 --- src/hg/utils/otto/otto.crontab +++ src/hg/utils/otto/otto.crontab @@ -1,88 +1,88 @@ # DO NOT EDIT THE OTTO CRONTAB FILE DIRECTLY! # This file is in the kent git repository: ~/kent/src/hg/utils/otto/otto.crontab # Please edit and commit changes to the git repository, # and then ssh otto@hgwdev and run crontab on the edited and checked in file, # for example crontab ~lrnassar/kent/src/hg/utils/otto/otto.crontab TMPDIR=/data/tmp ottomeister=lrnassar@ucsc.edu #Format: Minute - Hour - DayofMonth month Day-of-week MAILTO=lrnassar@ucsc.edu #Daily sandbox update 41 07 * * 1-5 /cluster/home/otto/bin/sandboxupdate # save shell history and last log into log files in ~/lastLog/ # last day of the month to catch them just before log rotation 38 23 30 4,6,9,11 * ~/lastLog/lastLog.sh 38 23 31 1,3,5,7,8,10,12 * ~/lastLog/lastLog.sh 38 23 28 2 * ~/lastLog/lastLog.sh 38 23 29 2 * ~/lastLog/lastLog.sh ####################################################### ###################### OTTO ########################### ####################################################### SHELL=/bin/sh PATH=/cluster/bin/scripts:/cluster/bin/x86_64:/usr/local/bin:/bin:/usr/bin MAILTO=lrnassar@ucsc.edu #Update check 0 5 1 */3 * mail -s "OMIM/GWAS CHECK - DID DBSNP UPDATE?" lrnassar@ucsc.edu < /cluster/home/chmalee/crontabs/dbSnpCheck.txt #DECIPHER #11 4 * * * /hive/data/outside/otto/decipher/decipherWrapper.sh #GWAS Catalog 41 4 * * 3 /hive/data/outside/otto/gwas/gwasWrapper.sh #GeneReviews 00 8 * * 2 /hive/data/outside/otto/geneReviews/geneReviewsWrapper.sh #LRG 57 9 1 * * /hive/data/outside/otto/lrg/lrgWrapper.sh #dbVar 13 8 2 * * /hive/data/outside/otto/dbVar/dbVarWrapper.sh #Orphanet 10 7 10 * * /hive/data/outside/otto/orphanet/orphanetWrapper.sh #ClinVar MAILTO=max@soe.ucsc.edu,lrnassar@ucsc.edu 08 00 8 * * umask 002; /hive/data/outside/otto/clinvar/doUpdate.sh #OMIM 17 4 * * * /hive/data/outside/otto/omim/omimWrapper.sh 2>&1 #LOVD 14 13 * * mon /hive/data/outside/otto/lovd/doUpdate.sh #Mastermind 05 8 8 */3 * /hive/data/outside/otto/mastermind/buildMastermind.sh #wuhCor1 uniprot otto cron by Max, May 2021 00 4 * * * /hive/data/outside/otto/uniprot/covidCheck.sh #User annotations #* * * * * ~max/miniconda3/envs/py3/bin/python ~max/usr/scripts/tsvSafeToBigBed /cluster/home/max/.user-annots-browser-track-c513a43ffff8.json https://docs.google.com/spreadsheets/d/1l38ypTcQH2AP2hlBmQ7kIXz1G4e33RPX-iFH1vu-utU/edit#gid=0 ~max/public_html/userAnnots/public.bb #ClinGen MAILTO=abenet@ucsc.edu,lrnassar@ucsc.edu 00 9 * * * /hive/data/outside/otto/clinGen/clinGenWrapper.sh #GRC Incident -#MAILTO=lrnassar@ucsc.edu,hiram@soe.ucsc.edu -#33 09 * * * /hive/data/outside/grc/incidentDb/runUpdate.sh makeItSo +MAILTO=lrnassar@ucsc.edu,hiram@soe.ucsc.edu +33 09 * * * /hive/data/outside/otto/grcIncidentDb/runUpdate.sh makeItSo #NCBI RefSeq #MAILTO=lrnassar@ucsc.edu,hiram@soe.ucsc.edu #23 8 * * 3 /hive/data/outside/ncbi/genomes/ncbiRefSeq/ottoNcbiRefSeq.sh #OMIM Upload MAILTO=lrnassar@ucsc.edu HGDB_CONF=/cluster/home/otto/.hg.conf.beta 15 05 * * * /hive/data/outside/otto/omim/omimUploadWrapper.sh #Format: Minute - Hour - DayofMonth month Day-of-week