73db11cce7b606145e13f1d15b02651f27f58a91 max Wed Sep 16 06:18:38 2026 -0700 danioCode: relabel with full DANIO-CODE branding, un-nest conservation, default on one RNA-seq/ChIP-seq sample Rename the "DC" shortLabel prefix to "DANIO-CODE" throughout (labels were getting long, but the full name matters more than brevity here). Relabel the danioCode superTrack itself to "DANIO-CODE Elements" and drop the now-redundant DANIO-CODE prefix from its remaining nested composites (Elements, Cell Types, COPEs DOPEs, Enhancers, Promoters). Un-nest the Burgess lab's phastCons/CNE conservation data (dcComparativeGenomics) into its own top-level track, "Burgess Fish PhastCons", group compGeno -- same treatment as the CRISPR tracks pulled out earlier, since this isn't DANIO-CODE's own data either. Rewrote every description page's intro: dropped the internal link to the superTrack in favor of a line crediting the DANIO-CODE project and linking to https://danio-code-dcc.genereg.net/, cut each intro to two sentences or fewer, and dropped the general explainer paragraphs (what non-coding regulation is, what conservation is) from danioCode.html and the conservation page entirely. Turn on exactly what the hub itself already marked "on": one RNA-seq sample (Prim-5, Busch-Nentwich lab) and one ChIP-seq signal track (H3K4me3), by letting dcRNAseqComposite and dcChIPseqComposite keep the hub's own "visibility full" instead of forcing hide, via VISIBLE_BY_DEFAULT in danioCodeHubToRa.py. Everything else (hundreds more subtracks per composite) stays off by default. tdbQuery -check passes; still alpha only. refs #38265 diff --git src/hg/makeDb/doc/danRer11/danioCode.txt src/hg/makeDb/doc/danRer11/danioCode.txt index 3d2290b4127..671de9ee787 100644 --- src/hg/makeDb/doc/danRer11/danioCode.txt +++ src/hg/makeDb/doc/danRer11/danioCode.txt @@ -173,15 +173,64 @@ # restructuring only moves stanzas around and adds one synthetic superTrack # stanza, it drops nothing new) cp danioCode.ra ~/kent/src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.ra # tdbQuery -check requires a superTrack's own children to sit contiguously right # after it in the file -- an unrelated top-level track (one of the newly # standalone composites) sitting between danioCode and one of its remaining # children fails with "X comes between parent (danioCode) and child (Y)". So # TOP_ORDER emits danioCode's own children (NESTED_ORDER) immediately after the # danioCode stanza, then the standalone tracks, then dcCrispr. cd ~/kent/src/hg/makeDb/trackDb tdbQuery -check "select count(*) from danRer11" # no errors; still alpha-only via "include danioCode.ra alpha" in # zebrafish/danRer11/trackDb.ra, so none of this reaches beta/public yet. + +# 2026-09-16 Claude max - relabel and un-nest the Burgess lab conservation track +# +# danioCode superTrack shortLabel -> "DANIO-CODE Elements" (was "DANIO-CODE") +# dcComparativeGenomics (phastCons + CNE, Burgess lab) -> un-nested into its own +# top-level track, shortLabel "Burgess Fish PhastCons", group compGeno +# (Comparative Genomics), alongside dcCrispr as the two Burgess-lab tracks +# distributed via the DANIO-CODE hub but not DANIO-CODE's own data +# the five remaining nested composites (comp, comp_cell_type, copes_and_dopes, +# evalidation, consensus_promoters) drop the "DANIO-CODE " shortLabel prefix, +# since it is now redundant with the superTrack's own label +# +# Implemented in TOP_LABELS / STANDALONE_GROUP / NESTED_ORDER in +# danioCodeHubToRa.py, then regenerated the same way as before: + +cd /hive/data/genomes/danRer11/bed/danioCode +~/kent/src/hg/makeDb/scripts/danioCode/danioCodeHubToRa.py \ + trackDb.txt \ + https://trackhub2.genereg.net/DANIO-CODE/danRer11/ \ + danioCode.ra \ + --drop-list missingUrls.txt \ + --local-prefix /gbdb/danRer11/danioCode +cp danioCode.ra ~/kent/src/hg/makeDb/trackDb/zebrafish/danRer11/danioCode.ra +cd ~/kent/src/hg/makeDb/trackDb +tdbQuery -check "select count(*) from danRer11" +# no errors + +# Also rewrote every description page's intro: dropped the internal link to the +# superTrack in favor of a line crediting the DANIO-CODE project and linking to +# https://danio-code-dcc.genereg.net/, cut each intro to two sentences or fewer, +# and for danioCode.html and dcComparativeGenomics.html (now "Burgess Fish +# PhastCons") dropped the general explainer paragraphs (what non-coding +# regulation is, what conservation is) entirely. + +# Loaded into the personal sandbox to review before committing: +cd ~/kent/src/hg/makeDb/trackDb +make DBS=danRer11 update +# Loaded 2041 track descriptions total; tdbQuery -check clean + +# 2026-09-16 Claude max - turn on one RNA-seq and one ChIP-seq sample by default +# +# Everything was visibility hide (see the note above, still open on #38239 for +# most of the collection). dcRNAseqComposite and dcChIPseqComposite each already +# had exactly one subtrack marked "on" by the hub itself (an RNA-seq sample and +# an H3K4me3 ChIP-seq signal track), so let those two composites keep the hub's +# own "visibility full" instead of forcing hide -- one sample per composite +# shows by default, not the whole pile (RNA-seq alone has 544 subtracks). +# VISIBLE_BY_DEFAULT in danioCodeHubToRa.py controls which composites this +# applies to; regenerated the same way as before and reloaded trackDb_max.