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 $D, and hgTrackDb -strict drops any member whose file is missing, so each assembly gets only the tracks that were built for it: STRchive on all three, the other four on hg38 only. The description page is rewritten for the new evidence-level coloring, gains an evidence filter, and now says that the track updates itself and that older versions are on GitHub rather than here. All of that is alpha only. Nothing copies /gbdb/*/strVar/ out to the RR yet, so releasing this trackDb would have it promise data the RR does not have. The old hg38-only version stays as human/hg38/strVar.ra, tagged beta,public, until the sysadmins install the strchiveAutoPush cron drafted alongside the otto job. The header of strVarNew.ra lists what to delete and rename then. refs #38268 diff --git src/hg/makeDb/doc/hg38/strchive.txt src/hg/makeDb/doc/hg38/strchive.txt index e84305e520d..668676069b9 100644 --- src/hg/makeDb/doc/hg38/strchive.txt +++ src/hg/makeDb/doc/hg38/strchive.txt @@ -1,32 +1,64 @@ # STRchive disease-associated STR loci track (part of strVar supertrack) # 2026-03-12 (max) # Data from STRchive (https://strchive.org/), CC BY 4.0 # Paper: Hiatt et al. Genome Med 2025, PMID 40140942 # 75 disease-associated tandem repeat expansion loci # Curated from published literature by the Dashnow lab # Source: downloaded from GitHub mkdir -p /hive/data/genomes/hg38/bed/str/strchive cd /hive/data/genomes/hg38/bed/str/strchive wget https://raw.githubusercontent.com/dashnowlab/STRchive/refs/heads/main/data/catalogs/STRchive-disease-loci.hg38.general.bed # Convert to BED9+ format (colored by inheritance mode) python3 ~/kent/src/hg/makeDb/scripts/strchive/strchiveToBed.py \ STRchive-disease-loci.hg38.general.bed > strchive.bed 2>/dev/null # Sort and convert to bigBed bedSort strchive.bed strchive.bed bedToBigBed strchive.bed /hive/data/genomes/hg38/chrom.sizes strchive.bb \ -type=bed9+ -tab -as=$HOME/kent/src/hg/makeDb/scripts/strchive/strchive.as # Symlink into /gbdb (under webstr/ directory with other STR tracks) ln -sf /hive/data/genomes/hg38/bed/str/strchive/strchive.bb /gbdb/hg38/webstr/strchive.bb # trackDb: strchive track is inside the strVar supertrack # trackDb entry: ~/kent/src/hg/makeDb/trackDb/human/hg38/webstr.ra # HTML doc: ~/kent/src/hg/makeDb/trackDb/human/hg38/strchive.html # Load trackDb cd ~/kent/src/hg/makeDb/trackDb make DBS=hg38 + +############################################################################# +# STRchive is now an otto track, on hg19/hg38/hs1 +# 2026-09-04 (max) + +# Everything above is history. STRchive now builds a Genome Browser bigBed for +# every release and publishes it on their GitHub releases page, so there is no +# conversion left to do on our side - see dashnowlab/STRchive#333. An otto job +# checks weekly for a new release and repoints the /gbdb symlinks at it: + +# kent/src/hg/utils/otto/strchive/ script, makefile, README +# /hive/data/outside/otto/strchive/ where it runs, and where the data lives +# otto.crontab 45 7 * * 1 + +# Do not rebuild by hand. To force an update or roll back: +# /hive/data/outside/otto/strchive/strchiveOtto.py --force +# /hive/data/outside/otto/strchive/strchiveOtto.py --release v2.26.1 + +# Their release ships hg19, hg38 and T2T-chm13 (= hs1) files and we take all +# three, so the track is on three assemblies now. The trackDb stanza moved from +# human/hg38/strVar.ra to human/strVar.ra and uses $D in the bigDataUrls, so +# hgTrackDb -strict gives each assembly only the strVar members whose file is +# actually there. strVar.html and strchive.html moved up to human/ with it. + +# /gbdb/<db>/strVar/strchive.bb -> the otto releases dir, one symlink per db +# /gbdb/<db>/strVar/strchive.version.txt is what the dataVersion setting shows + +# The new trackDb is alpha-only until the auto-push exists: without a cron +# copying /gbdb/*/strVar/ out to the RR, a released trackDb would promise data +# the RR does not have. human/strVarNew.ra is tagged alpha, human/hg38/strVar.ra +# is tagged beta,public and still describes the old hg38-only track. Release +# steps are in the header of strVarNew.ra. refs #38268