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 ", but stanzas are now indented and read "parent 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 @@ -1,78 +1,83 @@ # 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 $CBHUB_OUT, NOT next to the scripts (that dir is +# git-controlled). Default: /hive/users/mspeir/claude/cell-browser/all-tracks-hub-build +# # The per-track source files (abs_path column of manifest.tsv) are the files the # Cell Browser datasets already serve; nothing is regenerated here, only copied. ############################################################################## # 2. Copy the data files into place (bed dir, served via a /gbdb symlink) ############################################################################## # Every subtrack of the cellBrowserHg38 composite is copied into # /hive/data/genomes/hg38/bed/singleCellSignalsPeaks/ # keeping each file's served relative path (e.g. # human-enhancer-atlas/.../Adipocyte.bw , # allen-brain-science/seaad_MTG/bw/ADNC0Astro.bw ). # The served subpath is preserved on purpose: 18 peak-file basenames repeat # across datasets (cortex-atac), so a flat directory would clobber them. # 936 files total (bigWig + bigBed/bigNarrowPeak), ~206 GB. # # The file list comes straight from the composite's bigDataUrl lines mapped back # to manifest abs_paths; copy each abs_path to bed/ (mkdir -p parents). ############################################################################## # 3. Generate the trackDb .ra ############################################################################## # makeSingleCellSignalsPeaksRa.py reads the hub's hg38 stanzas, keeps the # cellBrowserHg38 subtracks, renames the composite to singleCellSignalsPeaks, # repoints every bigDataUrl at the local /gbdb copy, and writes the .ra with # group=regulation (ATAC signal/peaks sit with the ENCODE regulatory tracks). # Subtrack colors and labels (incl. the SEA-AD subclass colors) carry through. # # scriptDir=$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: