793f652411c510eaf02426d5c36dc599d02dd42f rhead Wed Sep 21 16:58:58 2011 -0700 Finally checking in the crontabs that belong to the qateam user, which we depend on for a lot. Redmine #404. diff --git build/crontabs/qateam/hgwdev.crontab build/crontabs/qateam/hgwdev.crontab new file mode 100644 index 0000000..cd6d415 --- /dev/null +++ build/crontabs/qateam/hgwdev.crontab @@ -0,0 +1,131 @@ +# specifying path so that the "which" command will work within qa scripts. +PATH=/cluster/bin/scripts:/cluster/bin/x86_64:/usr/local/bin:/bin:/usr/bin:/cluster/bin/i386 +# (added /cluster/bin/i386 to the path because it has ipw command, which catchBot.csh uses - BLR) + +# Minute Hour DOM Month DOW command + +MAILTO=rhead + +#### Jobs that were running on qateam crontab long before June 2010 (BLR): +3 3 15 2,6,10 * echo "This is the tri-annual reminder to check with Jim and Galt about the BLAT executable to see if there are any upgrades worth installing on our servers." | mail -s "check for BLAT updates" qateam + + +#### Jobs that ran on Angie's crontab until June 2010 (BLR): +SHELL=/bin/csh +# m h da mo dow +# This refresh is now taken care of via a root cron job 2010-11-04 - Hiram +# refresh custom tracks referenced by saved sessions (this is for genome-test): +# 30 23 * * * setenv HGDB_CONF /cluster/home/qateam/.hg.conf.include; /cluster/bin/x86_64/refreshNamedSessionCustomTracks hgcentraltest + +MAILTO=rhead,fanhsu +# unigene update for human SAGE track (running from /cluster/home/angie/unigeneVers/ prior to 6/23/10) +03 01 * * * /cluster/bin/scripts/unigene.csh + +MAILTO=browser-staff +# look for broken links in /gbdb and goldenPath: +26 01 * * * find /gbdb/ -mindepth 1 -maxdepth 1 -not -regex '^/gbdb/\(visiGene\|zoo3\).*' | xargs findBrokenLinks.csh +MAILTO=galt,rhead +26 03 30 1,6 * findBrokenLinks.csh /gbdb/visiGene +MAILTO=encode-staff@soe.ucsc.edu,rhead@soe.ucsc.edu +56 01 * * * findBrokenLinks.csh /usr/local/apache/htdocs-hgdownload/goldenPath |& grep -v fish.seq15jun2001 + +MAILTO=rhead +# checkHgFindSpec -checkTermRegex +03 03 * * * /cluster/home/qateam/bin/scripts/runCheckHgFindSpec > /usr/local/apache/htdocs-genecats/qa/test-results/checkHgFindSpec/hgwdevOutput + +# monitoring job inherited by angie from Heather: +4 * * * * apacheMonitor genome-log apachelog 60 + + +#### Jobs that ran on b0b's crontab until June 2010 (BLR): +# alert relevant people of B-queue content +10 05 12 * * /cluster/bin/scripts/alertBqueue.csh go + +# check for new tables daily +20 02 * * * /cluster/bin/scripts/findNewTables.csh hg19,hg18,mm9 | mail -s "new tables yesterday" rhead@soe.ucsc.edu pauline@soe.ucsc.edu katrina@soe.ucsc.edu + +# run sessionStats.csh monthly +20 12 1 * * /cluster/bin/scripts/sessionStats.csh go | mail -s "monthly sessionStats" angie@soe.ucsc.edu rhead@soe.ucsc.edu kuhn@soe.ucsc.edu + +# run linkCheck on everything monthly (broken 2008-10-10) +#######20 4 10 * * /cluster/bin/scripts/cronLinks.csh go | mail -s "linkCheck" kuhn@soe.ucsc.edu pauline@soe.ucsc.edu + +# check RR processes several times per workday: +10 9,11,13,15,17 * * 1-5 /cluster/bin/scripts/showProcesslist.csh go | mail -s "showProcesslist" rhead@soe.ucsc.edu + +# check STATUS dumps on Mondays: +04 02 * * 1 /cluster/bin/scripts/checkTableStatus.csh | mail -s "TABLE STATUS dump" rhead@soe.ucsc.edu + +# check genbank every tuesday morning: +40 06 * * 4 /cluster/bin/scripts/realTime.csh hg18 gbCdnaInfo | mail -s "realTime genbank weekly check, hg18" rhead@soe.ucsc.edu + +# keep a dump of all hgcentral tables monthly +40 22 1 * * /cluster/bin/scripts/backupCentral.csh go% | mail -s "save hgcentral monthly" rhead@soe.ucsc.edu + +# m h da mo dow +# increment databaseAday: +03 00 * * 1-5 /cluster/bin/scripts/databaseAday.csh next +11 00 * * 1-5 /cluster/bin/scripts/databaseAday.csh today | mail -s "new database today" rhead@soe.ucsc.edu + +# check uiLinks on hgwbeta for today's db (and grep out the "doesn't exist" errors caused by multi-view pages): +33 00 * * 1-5 /cluster/bin/scripts/checkTrackUiLinks.csh `/cluster/bin/scripts/databaseAday.csh today` all |& grep -v "doesn[']t exist" > /usr/local/apache/htdocs-genecats/qa/test-results/uiLinks/`/cluster/bin/scripts/databaseAday.csh today` +55 00 * * 1-5 echo " http://genecats.cse.ucsc.edu/qa/test-results/uiLinks/`/cluster/bin/scripts/databaseAday.csh today`" | mail -s "today's ui link check" rhead luvina + +# check a database daily for sync: +32 01 * * 1-5 /cluster/bin/scripts/syncAday.csh go | mail -s "sync for today" greg + +# do a realTime on db o' the day to get it in cache: +12 05 * * 1-5 /cluster/bin/scripts/realTime.csh `/cluster/bin/scripts/databaseAday.csh today` gbLoaded | mail -s "gbLoaded sync for `/cluster/bin/scripts/databaseAday.csh today`" rhead@soe.ucsc.edu + +# run a metadata check on the db o' th' day: +46 03 * * 1-5 /cluster/bin/scripts/checkMetaAday.csh go | mail -s "metadata on `/cluster/bin/scripts/databaseAday.csh today`" rhead + +# store /gbdb dump from beta: +23 00 * * * /cluster/bin/scripts/checkGbdbDiffs.csh go | mail -s "/gbdb dump" rhead@soe.ucsc.edu + +# check site usage: +56 2,7,15 * * 1-5 /cluster/bin/scripts/catchBot.csh 50000 10 | mail -s "catchBot 50000" rhead +55 5 * * * /cluster/bin/scripts/catchBot.csh 10000 10 | mail -s "catchBot 10000" rhead + +# m h da mo dow +# check trackDbs early monday morning: +14 6 * * 1 /cluster/bin/scripts/trackDbGlobal.csh hgw2 realTime | mail -s "trackDbGlobal" rhead ann pauline mary greg luvina steve + + +#### Jobs that ran on ann's crontab until June 2010 (BLR): +# check to see if there are new files to go with the CGI push +3 3 * * 3 /cluster/home/qateam/bin/scripts/findCgiFiles.csh go + +# check to see what kind of browsers and o/s people are using to access the public website +44 4 * * 0 /cluster/bin/scripts/browserUsage.csh go; echo "http://genecats.cse.ucsc.edu/qa/test-results/browserUsage/?C=M;O=D" | mail -s "browser usage script ran" rhead + +MAILTO=browser-staff@soe.ucsc.edu +# check the integrity of the trackDb.ra files +5 6 * * 1-5 tdbQuery -check -strict "select count(*) from *" >/dev/null +10 6 * * 1-5 tdbQuery -check -release=beta -strict "select count(*) from *" >/dev/null +15 6 * * 1-5 tdbQuery -check -release=public -strict "select count(*) from *" >/dev/null + +MAILTO=rhead +#### new jobs!: +# Update the qateam sandbox +# the script contains an email address for sending git reports to... currently this is 'rhead' +22 4 * * 1-5 /cluster/home/qateam/bin/scripts/DailySandboxUpdate > /dev/null + +MAILTO=rhead,hiram +# Check the source tree for duplicate case-independent filenames. These wreck havoc +# with git on the default case-independent Mac OS filesystem. (Redmine #403) +22 5 * * * cd ~qateam/kent; find . | tr '[A-Z]' '[a-z]' | sort | uniq -D + +MAILTO=rhead +# generate the tableDescriptions push request for all active dbs on the RR +32 12 * * 5 /cluster/home/qateam/bin/scripts/tabDescRequest | mail -s "push tableDescriptions" greg + +MAILTO=mary +# Check to see if genome-mysql is corrupted for the database a day +34 0 * * 1-5 checkGenomeMysql `databaseAday.csh today` +# Check to see if genome-mysql is corrupted for hg19, hg18 and mm9 everyday. +34 0 * * 1-5 checkGenomeMysql hg19 +34 0 * * 1-5 checkGenomeMysql hg18 +34 0 * * 1-5 checkGenomeMysql mm9 + +# Minute Hour DOM Month DOW command