4c06f1b66ceec8ba9e8f4618f632ccb271e2aa07 mspeir Wed Aug 12 15:15:20 2026 -0700 Adding line for Cell Browser differential expression worker, and moving cbAnnotServer line up to be next to some other CB cron lines, refs #24912 diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab index 9c32cadf840..bc115017146 100644 --- src/hg/utils/otto/otto.crontab +++ src/hg/utils/otto/otto.crontab @@ -157,33 +157,39 @@ #Add a new daily tip to the home page 5 5 * * 1-5 /cluster/software/bin/python /cluster/bin/scripts/generateTipOfDay.py -s ~/kent/src/hg/htdocs/allTipsRaw.html #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 0 0 * * 1-5 umask 002; ~bwick/miniconda3/bin/python3.8 ~bwick/cellBrowser/ucsc/updateNewsSec -r # Update Cell Browser .json facets files using tabulate_facets.pl 0 0 * * 1-5 cd /usr/local/apache/htdocs-cells-submit/facets && ~bwick/cellBrowser/ucsc/tabulate_facets.pl /usr/local/apache/htdocs-cells-beta/dataset.json 0 0 * * 1-5 cd /usr/local/apache/htdocs-cells-submit/facets && /usr/local/apache/htdocs-cells-submit/facets/tsv_to_json.py +# cbAnnotServer: Cell Browser login/annotation API (RM #37492). Keeps gunicorn +# (127.0.0.1:5051, Apache proxies /api to it) alive; restarts if down / on reboot. +* * * * * umask 002; CBANNOT_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/cbAnnot.env ~mspeir/cellBrowser/src/cbAnnotServer/deploy/watchdog.sh >> /hive/data/inside/cells/cbAnnotServer/logs/watchdog.log 2>&1 +@reboot umask 002; CBANNOT_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/cbAnnot.env ~mspeir/cellBrowser/src/cbAnnotServer/deploy/watchdog.sh >> /hive/data/inside/cells/cbAnnotServer/logs/watchdog.log 2>&1 + +# DE worker: Cell Browser differential expression (RM #24912). Keeps deWorker.py +# alive (reads the /hive job queue); restarts if down / on reboot. +* * * * * umask 002; DE_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/de.env ~mspeir/cellBrowser/src/cbAnnotServer/de/deploy/deWorkerWatchdog.sh >> +/hive/data/inside/cells/cbAnnotServer/logs/deWorker-watchdog.log 2>&1 +@reboot umask 002; DE_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/de.env ~mspeir/cellBrowser/src/cbAnnotServer/de/deploy/deWorkerWatchdog.sh >> +/hive/data/inside/cells/cbAnnotServer/logs/deWorker-watchdog.log 2>&1 # 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 && ./doUpdate.sh' MAILTO=cells@ucsc.edu @reboot umask 0000; /cluster/home/max/htdocs-cells-submit/tusd/tusd_linux_amd64/tusd -upload-dir /hive/data/inside/cells/upload/ -port 8443 -max-size 100000000000 - -# cbAnnotServer: Cell Browser login/annotation API (RM #37492). Keeps gunicorn -# (127.0.0.1:5051, Apache proxies /api to it) alive; restarts if down / on reboot. -* * * * * umask 002; CBANNOT_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/cbAnnot.env ~mspeir/cellBrowser/src/cbAnnotServer/deploy/watchdog.sh >> /hive/data/inside/cells/cbAnnotServer/logs/watchdog.log 2>&1 -@reboot umask 002; CBANNOT_ENV_FILE=/hive/data/inside/cells/cbAnnotServer/cbAnnot.env ~mspeir/cellBrowser/src/cbAnnotServer/deploy/watchdog.sh >> /hive/data/inside/cells/cbAnnotServer/logs/watchdog.log 2>&1