fe02c55d26614f1d5059c884fb2594f9b4d5ad50 mspeir Wed Aug 12 08:02:19 2026 -0700 singleCellSignalsPeaks: point at the hub build's new home, fix the file-copy script The hub build now lives in the cellBrowser repo under ucsc/allTracksHub, so the makeDocs link there instead of a personal work dir. HUB_BUILD in these scripts is the build's output dir, not its code; comments say so now, paths unchanged. copySingleCellSignalsPeaksFiles.py was silently copying nothing: it compared a whole line against "parent <composite>", but stanzas are now indented and read "parent <composite> off". Now dedents, matches the first token, and refuses to run on zero subtracks. Dry runs give 925 hg38 / 587 mm10, none missing. refs #37914 diff --git src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt index 966a7e92550..bd3a439151c 100644 --- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt +++ src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt @@ -1,100 +1,105 @@ # hg38 singleCellSignalsPeaks track - 2026-07-20 Claude (mspeir) refs #37820 # The native hg38 "singleCellSignalsPeaks" faceted composite is the Genome -# Browser version of the UCSC Cell Browser all-tracks super hub (Redmine #37820, -# built under /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build). It -# gathers the per-cell-type signal (bigWig) and peak (bigBed / bigNarrowPeak) +# Browser version of the UCSC Cell Browser all-tracks super hub (Redmine #37820). +# The hub build lives in the cellBrowser repo, ucsc/allTracksHub: +# https://github.com/ucscGenomeBrowser/cellBrowser/tree/develop/ucsc/allTracksHub +# +# It gathers the per-cell-type signal (bigWig) and peak (bigBed / bigNarrowPeak) # tracks from the single-cell ATAC datasets in the Cell Browser and re-parents # them under one faceted composite. cCREs and interactions live in their own # composites in the hub and are NOT part of this track. ############################################################################## # 1. Source data ############################################################################## # The track mirrors the hub's main hg38 signal-&-peaks faceted composite # (cellBrowserHg38). That composite and its facet metadata are produced by the # hub build from the Cell Browser dataset tree (/hive/data/inside/cells/datasets): # -# cd /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build +# cd $HOME/cellBrowser/ucsc/allTracksHub # python3 build_manifest.py # scan datasets -> manifest.tsv # python3 build_stanzas.py # manifest -> stanzas/hg38.trackDb.txt # # + meta/hg38.metadata.tsv # +# The build writes its output to $CBHUB_OUT, NOT next to the scripts (that dir is +# git-controlled). Default: /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build +# # The per-track source files (abs_path column of manifest.tsv) are the files the # Cell Browser datasets already serve; nothing is regenerated here, only copied. ############################################################################## # 2. Copy the data files into place (bed dir, served via a /gbdb symlink) ############################################################################## # Every subtrack of the cellBrowserHg38 composite is copied into # /hive/data/genomes/hg38/bed/singleCellSignalsPeaks/<served-relpath> # keeping each file's served relative path (e.g. # human-enhancer-atlas/.../Adipocyte.bw , # allen-brain-science/seaad_MTG/bw/ADNC0Astro.bw ). # The served subpath is preserved on purpose: 18 peak-file basenames repeat # across datasets (cortex-atac), so a flat directory would clobber them. # 936 files total (bigWig + bigBed/bigNarrowPeak), ~206 GB. # # The file list comes straight from the composite's bigDataUrl lines mapped back # to manifest abs_paths; copy each abs_path to bed/<relpath> (mkdir -p parents). ############################################################################## # 3. Generate the trackDb .ra ############################################################################## # makeSingleCellSignalsPeaksRa.py reads the hub's hg38 stanzas, keeps the # cellBrowserHg38 subtracks, renames the composite to singleCellSignalsPeaks, # repoints every bigDataUrl at the local /gbdb copy, and writes the .ra with # group=regulation (ATAC signal/peaks sit with the ENCODE regulatory tracks). # Subtrack colors and labels (incl. the SEA-AD subclass colors) carry through. # # scriptDir=$HOME/kent/src/hg/makeDb/scripts/singleCellSignalsPeaks # python3 $scriptDir/makeSingleCellSignalsPeaksRa.py \ -# --stanzas /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build/stanzas/hg38.trackDb.txt \ +# --stanzas $CBHUB_OUT/stanzas/hg38.trackDb.txt \ # --out $HOME/kent/src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra # # https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/singleCellSignalsPeaks ############################################################################## # 4. Facet metadata ############################################################################## # The faceted composite's metaDataUrl points at a copy of the hub's hg38 # main-faceted metadata (primaryKey = Track): # -# cp /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build/meta/hg38.metadata.tsv \ +# cp $CBHUB_OUT/meta/hg38.metadata.tsv \ # /hive/data/genomes/hg38/bed/singleCellSignalsPeaks/singleCellSignalsPeaks_metadata.tsv ############################################################################## # 5. Labels, colors, and facets ############################################################################## # The cell type / cell class / shortLabel / longLabel / color / facet values are # all derived by build_stanzas.py, not copied from the source hubs. That logic # (paper-curated cell-type crosswalks, the shared broad-class color palette, the # rebuilt short and long labels, the variant descriptors that keep every label # unique, and the per-collection tissue/life-stage/condition parsing incl. SEA-AD # region + ADNC) is documented once in doc/mm10/singleCellSignalsPeaks.txt # section 4; it runs identically for hg38. Tracks are colored by broad cell class # from the same palette as mm10, so a class is the same color on both assemblies. # # hg38-specific label notes: # - cortex-atac calls peaks three ways and serves all three for each cell type. # The method is a filename suffix on some files (AstroOligo_MACSpeaks.bb) and # the containing directory on others (MACSpeaks/AstroOligo.bb) -- both layouts # appear in the same dataset and the two files are genuinely different peak # sets, so both forms are detected and named in the label. # - human-enhancer-atlas rolls tissue-qualified fibroblast/endothelial clusters # (Fibro_Muscle, Endothelial_General_2) up to one cell type; the source code # goes in the label so the clusters stay distinguishable. # - SEA-AD shortLabels carry a compact region + ADNC token (Astrocyte MTG A0), # since the longLabel distinction alone would leave eight identical short # labels per cell type (2 regions x 4 ADNC levels). ############################################################################## # Counts ############################################################################## # 936 files resolved across 9 datasets: human-enhancer-atlas (444), # sea-ad-brain-atac (184), cortex-atac (91), retina (69), neuro-degen-atac (67), # multiomic-human-heart (40), cardiogenesis-atac (19), olg-eae-ms (18), # brainvar (4). 10 mislabeled interaction bigBeds (cortex-atac interact.old/) are # reclassified to the interact composite and 1 QC cluster is dropped, leaving 925 # subtracks in the track. Facet metadata rows match the subtracks 1:1. # All 925 longLabels are unique; shortLabels are <=22 chars with no underscores.