70ac948e82b41ef316523635c04e5e2c4a89c417 mspeir Fri Sep 4 16:57:54 2026 -0700 trackLists: give the variant frequency projects their own table, move the page to goldenPath/help/mirrorTracks.html, add the otto cron line, refs #37781 Half the restricted list was national sequencing cohorts sitting under varFreqs and phasedVars, and in one alphabetical table they buried the tracks people actually write in about, OMIM, HGMD and DECIPHER. Those cohorts now get a table of their own below the rest. The split is read off the trackDb parent chain, so the next cohort added under varFreqs lands in the right table with no edit here. The page moves off the htdocs root to goldenPath/help/mirrorTracks.html, beside mirror.html, which now links to it. That link goes in src/product/README.txt, the pandoc source mirror.html is generated from. The licensing page link follows the move, and the page title changes with the file name. Also adds the weekly otto line, placed above the HGDB_CONF that would otherwise apply to it, and keeps the job from listing itself as a self-updating track. Co-Authored-By: Claude Opus 5 (1M context) diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab index 68549e48fd0..7a9a636567c 100644 --- src/hg/utils/otto/otto.crontab +++ src/hg/utils/otto/otto.crontab @@ -145,30 +145,37 @@ ### verify liftOverChain and quickLiftChain tables have ### identical fromDb,toDb pairs: 11 3 * * * /hive/data/inside/GenArk/checkChainTables/toFromCounts.sh #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/python /cluster/bin/scripts/buildPublicSessionThumbnailsIndexPage.py /usr/local/apache/htdocs/ #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 +# Mirror-facing track lists (RM #37781): tracks we cannot redistribute, tracks +# that update themselves, tracks contributed from outside UCSC. Writes +# goldenPath/help/mirrorTracks.html into htdocs; reaching the RR needs a /root +# autoPush entry from cluster-admin. Weekly is plenty, none of the three lists +# moves daily. Silent unless a restricted file is found reachable on hgdownload. +32 6 * * 4 /hive/data/outside/otto/trackLists/trackLists.sh + #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 # Hidden-dataset reminders (RM #38246). Once a month, queue one draft email per # hidden dataset whose submitter has not been asked in a year, and mail the # report to cells@. Nothing reaches an author until a person reviews the queue