5812a4dccee9aacb8473bd9ccd04d6c78d82cb4c lrnassar Tue Nov 12 16:04:56 2024 -0800 Moving back the compare cron as it was running before the nightly build. No RM. diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab index c255de6..88feb77 100644 --- src/hg/utils/otto/otto.crontab +++ src/hg/utils/otto/otto.crontab @@ -1,131 +1,131 @@ # 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 # To save the current crontab back into git: # crontab -l > ~max/kent/src/hg/utils/otto/otto.crontab # logout # cd ~max/kent/src/hg/utils/otto/ # git commit otto.crontab -m 'updating crontab' # Note that you can see the list of auto-pushes of files from hgwdev to the RR by running: # cat /etc/crontab # on Hgwdev. TMPDIR=/data/tmp ottomeister=otto-group@ucsc.edu #Format: Minute - Hour - DayofMonth month Day-of-week MAILTO=otto-group@ucsc.edu #Daily sandbox update 41 00 * * 1-7 /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=otto-group@ucsc.edu #md5sum checker script - makes sure otto scripts in hive match git tree -0 0 * * 1-5 ~/kent/src/hg/utils/otto/ottoCompareGitVsHiveFiles.py +0 7 * * 1-5 ~/kent/src/hg/utils/otto/ottoCompareGitVsHiveFiles.py # PanelApp MAILTO=max@soe.ucsc.edu,otto-group@ucsc.edu 10 10 * * 2 /hive/data/outside/otto/panelApp/updatePanelApp #DECIPHER - Reactivated 5/13/2022 by Lou 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 4,6,12 * /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=otto-group@ucsc.edu 08 00 8 * * umask 002; /hive/data/outside/otto/clinvar/doUpdate.sh #MANE 11 5 * * 1 python3 /hive/data/outside/otto/mane/doMane.py #GenCC 8 16 * * 2 python3 /hive/data/outside/otto/genCC/doGenCC.py #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 * * /hive/data/outside/otto/mastermind/buildMastermind.sh # UniProt massive 110+ database update, takes 3-4 days. #Format: Minute - Hour - DayofMonth month Day-of-week MAILTO=max@soe.ucsc.edu,otto-group@ucsc.edu 00 07 26 * * /hive/data/outside/otto/uniprot/doUpdate.sh run #wuhCor1 uniprot otto cron by Max, May 2021 00 4 * * * /hive/data/outside/otto/uniprot/covidCheck.sh #ClinGen 00 9 * * * /hive/data/outside/otto/clinGen/clinGenWrapper.sh #ClinGen CSpec 11 11 * * 3 /hive/data/outside/otto/clinGen/clinGenCspec/makeClinGenCspec.sh #GRC Incident MAILTO=hiram@soe.ucsc.edu,otto-group@ucsc.edu 33 06 * * * /hive/data/outside/otto/grcIncidentDb/runUpdate.sh makeItSo # GenArk update hgcentral.genark table, once a week on Tuesday # the script itself sends email for notices about activity 37 10 * * 2 /hive/data/inside/GenArk/updateHgcentral.sh makeItSo #NCBI RefSeq 23 8 * * 3 /hive/data/outside/otto/ncbiRefSeq/ottoNcbiRefSeq.sh #Index page public session thumbnails update MAILTO=otto-group@ucsc.edu 11 1 * * 4 /cluster/software/bin/python3.6 /cluster/bin/scripts/buildPublicSessionThumbnailsIndexPage.py /usr/local/apache/htdocs/ #OMIM Upload HGDB_CONF=/cluster/home/otto/.hg.conf.beta 15 05 * * * /hive/data/outside/otto/omim/omimUploadWrapper.sh MAILTO=cells@ucsc.edu # Cell Browser news sec update by Matt/Brittney Sept 2022 04 12 * * 1-5 ~bwick/miniconda3/bin/python3.8 ~bwick/cellBrowser/ucsc/updateNewsSec -r # Malacards update. Not done monthly, but running monthly anyways, as they don't have a fixed schedule #Format: Minute - Hour - DayofMonth month Day-of-week MAILTO=mhaeussl@ucsc.edu 04 04 20 * * /hive/data/outside/otto/malacards/update.sh MAILTO=jbirgmei@ucsc.edu # PubTator3 dbSNP track update 28 08 * * * /bin/zsh -c 'cd /hive/data/outside/otto/pubtatorDbSnp && ./BUILD'