60eff7582a4de0728a2f2d7b9d1cd417502e8ed3 Merge parents 9bd482f b139dda kent Wed Nov 24 14:36:10 2021 -0800 Fix merge conflict from both adding new stuff at same place. diff --cc src/hg/utils/otto/otto.crontab index e1bc4ce,639c75a..0000000 deleted file mode 100644,100644 --- src/hg/utils/otto/otto.crontab +++ /dev/null @@@ -1,88 -1,85 +1,0 @@@ --# 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 -- --#OMIM Upload --HGDB_CONF=/cluster/home/otto/.hg.conf.beta --15 05 * * * /hive/data/outside/otto/omim/omimUploadWrapper.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 -- --#NCBI RefSeq --#MAILTO=lrnassar@ucsc.edu,hiram@soe.ucsc.edu --#23 8 * * 3 /hive/data/outside/ncbi/genomes/ncbiRefSeq/ottoNcbiRefSeq.sh -- -- --#Format: Minute - Hour - DayofMonth month Day-of-week