0871110b9e07cfb8001e6de9d156e7e7f74f8c25 max Fri Sep 4 17:00:53 2026 -0700 STRchive track now updates itself, and is on hg19 and hs1 as well as hg38 STRchive builds a Genome Browser bigBed with every release now and publishes it on their GitHub releases page, so there is nothing left for us to convert. A new otto job checks weekly for a new release, downloads the file into its own releases/<tag> directory, sanity-checks the locus count, and repoints the /gbdb symlinks at it. Silent when there is no new release. See STRchive issue 333 for the correspondence that set this up. Their releases carry hg19, hg38 and T2T-chm13 (= hs1) files and we take all three, so the new strVar stanza lives in human/strVarNew.ra rather than under hg38. The bigDataUrls use $D, and hgTrackDb -strict drops any member whose file is missing, so each assembly gets only the tracks that were built for it: STRchive on all three, the other four on hg38 only. The description page is rewritten for the new evidence-level coloring, gains an evidence filter, and now says that the track updates itself and that older versions are on GitHub rather than here. All of that is alpha only. Nothing copies /gbdb/*/strVar/ out to the RR yet, so releasing this trackDb would have it promise data the RR does not have. The old hg38-only version stays as human/hg38/strVar.ra, tagged beta,public, until the sysadmins install the strchiveAutoPush cron drafted alongside the otto job. The header of strVarNew.ra lists what to delete and rename then. refs #38268 diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab index 7a9a636567c..f0ab527e0e9 100644 --- src/hg/utils/otto/otto.crontab +++ src/hg/utils/otto/otto.crontab @@ -75,30 +75,35 @@ #early-month run catches the previous month's update (no-ops if unchanged) 22 6 5 * * /hive/data/outside/otto/g2p/g2pWrapper.sh #OMIM 17 4 * * * /hive/data/outside/otto/omim/omimWrapper.sh 2>&1 #LOVD 14 13 * * mon /hive/data/outside/otto/lovd/doUpdate.sh #MitoMap 55 8 * * 3 /hive/data/outside/otto/mitoMap/checkMitoMapUpdate.sh #RefSeq Historical update notifier (RM #35766) - silent unless NCBI has a new release 40 8 * * 3 /hive/data/outside/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh +#STRchive - hg38 disease-associated tandem repeats, dashnowlab/STRchive#333. +#Weekly check for a new GitHub release, silent unless STRchive published one. +#STRchive releases one to two times a month. +45 7 * * 1 umask 002; /hive/data/outside/otto/strchive/strchiveOtto.py + # InSiGHT VCEP ClinVar curated variants weekly update 08 03 * * 2 umask 002; /hive/data/outside/otto/insight/doUpdate.sh # VCEP hub spec version notifier (RM #37795) - monthly, silent unless one of our # VCEP hub description pages is behind the ClinGen CSpec registry MAILTO=otto-group@ucsc.edu 40 06 15 * * /hive/data/outside/otto/vcepVersions/checkVcepVersions.py # 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