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