a64bc5a6cfe9756104a86f633b0f0a01772c4b83
lrnassar
  Wed Oct 6 16:55:59 2021 -0700
Updating a few things on otto. For the most part these are changes to the wrapper emails, which had not been updated in git, and the big changes are were done by engineers directly to the hive copy without updating the tree version. The big updates for clinvar were Max, and decipher was Braney I believe. To clarify, these now updated versions are the ones that have been running daily/weekly, so all of it has been in action already.

diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab
index 43a9416..e16746f 100644
--- src/hg/utils/otto/otto.crontab
+++ src/hg/utils/otto/otto.crontab
@@ -1,61 +1,65 @@
 #Below is the otto crontab active in the otto-meister's own cron
 #Changes here must be copied over by the current otto-meister
 
 #######################################################
 ###################### OTTO ###########################
 #######################################################
 
+SHELL=/bin/sh
+PATH=/cluster/bin/scripts:/cluster/bin/x86_64:/usr/local/bin:/bin:/usr/bin
+MAILTO=lrnassar@ucsc.edu
+
 #ISCA - Deprecated
 31 4 * * *  /hive/data/outside/otto/isca/iscaWrapper.sh 2>&1
 
 #OMIM
 MAILTO=max@soe.ucsc.edu,lrnassar@ucsc.edu
 17 4 * * *  /hive/data/outside/otto/omim/omimWrapper.sh 2>&1
 
 #Update check
 MAILTO=lrnassar@ucsc.edu
 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
 
 #ClinVar
 MAILTO=max@soe.ucsc.edu,lrnassar@ucsc.edu
 08 00 8 * * umask 002; /hive/data/outside/otto/clinvar/doUpdate.sh
 
 #LOVD
 14 13 * * mon /hive/data/outside/otto/lovd/doUpdate.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
 
 #Mastermind
 MAILTO=max@soe.ucsc.edu,lrnassar@ucsc.edu
 05 8 8  */3 * /hive/data/outside/otto/mastermind/buildMastermind.sh
 #
 #dbVar
 MAILTO=lrnassar@ucsc.edu
 13 8 2 * * /hive/data/outside/otto/dbVar/dbVarWrapper.sh
 
 #OMIM Upload
 HGDB_CONF=/cluster/home/lrnassar/.hg.conf.beta
 MAILTO=lrnassar@ucsc.edu
 15 05 * * *  /hive/data/outside/otto/omim/omimUploadWrapper.sh
 
 #ClinGen
 MAILTO=abenet@ucsc.edu,lrnassar@ucsc.edu
 00 9 * * * /hive/data/outside/otto/clinGen/clinGenWrapper.sh
 
 # wuhCor1 uniprot otto cron by Max, May 2021
 MAILTO=max@soe.ucsc.edu,lrnassar@ucsc.edu
 00 4 * * * /hive/data/outside/otto/uniprot/covidCheck.sh