File Changes for mspeir

v503_preview2 to v503_base (2026-08-24 to 2026-08-31) v503

• src/hg/cirm/cdw/httpsGatewayConfig/README.txt
  • lines changed 5, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/README
  • lines changed 4, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/help/cirmBasics.html
  • lines changed 8, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/js/cirmStuff.js
  • lines changed 3, context: html, text, full: html, text
    72ab5ade9fcc72e242d987bb84c92df08ba7601b Thu Aug 27 11:10:59 2026 -0700
    CIRM: remove references to the retired cirmdcm.soe.ucsc.edu host, refs #38191 cirmdcm.soe.ucsc.edu was the private server CESCG labs used to reach their prepublication data. It is retired, no longer answers on port 80 or 443, and is not being replaced. - cirmBasics.html: drop the "private server" paragraph from the Accounts section, adjust the heading and table of contents to match, and unlink the dead URL in the commented-out video block. - cirmStuff.js: drop the cirmdcm and cirm-01 clauses from isSecureSite(). cirm-01 was the same machine internally. hgwdev and sspsygene are unaffected. - gateway/htdocs/README: remove the dead login-for-testing URL and stop using the retired host as an example. proxy-host.conf is kept: it is the Apache config that stood the gateway up and the README beside it is the recipe that installs it. That README now says up front that the host is retired. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 18, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt
  • lines changed 36, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 8, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 50, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt
  • lines changed 87, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 12, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    05e212467751884f63353f671cf97c3f83f7a8a8 Fri Aug 28 14:47:20 2026 -0700
    singleCellSignalsPeaks mm10 makeDoc: correct the autoScale subtrack counts, refs #37914 Matches the corrected DROP_KEYS note in the hub build (cellBrowser ucsc/allTracksHub/build_stanzas.py): 475 subtracks corpus-wide (402 hg38, 73 mm10) inherited `autoScale group` from their source hubs, and a further 677 (184 hg38, 493 mm10) carried `autoScale on`, so build_stanzas drops autoScale for all 1152. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/build_celltype_crosswalks.py
  • lines changed 8, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-class.tsv
  • lines changed 9, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/celltype-palette.tsv
  • lines changed 1, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/celltype-crosswalks/paper-decodes/hg38_ct_class.tsv
  • lines changed 1, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/copySingleCellSignalsPeaksFiles.py
  • lines changed 72, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py
  • lines changed 8, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
  • lines changed 19, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 64, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra
  • lines changed 1461, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    6c09237078e2ea2fd7c383babc73a8f3b379202e Thu Aug 27 15:35:40 2026 -0700
    Risk Loci in Alzheimers peak track was duplicated. Removed duplicate. refs #37914
  • lines changed 341, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.html
  • lines changed 10, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 87, context: html, text, full: html, text
    3aac3982aa2b300c100086920451b2dc98a7f2b9 Fri Aug 28 14:49:32 2026 -0700
    singleCellSignalsPeaks: drop 5 superseded hg38 subtracks, alphabetize the references, refs #37820 The hg38 .ra is regenerated from the hub build, 934 -> 929 subtracks: - the 4 combined-stage BrainVar gene-activity tracks, superseded by the prenatal/postnatal pair of the same cell type, so every remaining BrainVar track now carries a life stage - neuro-degen-atac/peaks.bb, superseded by peaks.v2.bb (that dataset's hub.txt comments the peaks.bb bigDataUrl out and serves v2). The two collided on one track id and shipped as two indistinguishable "All cell types, peaks" tracks; with the collision gone the survivor is named ..._peaks and its label loses the "(peaks)" disambiguator. The exclusion itself lives in the hub build's new exclude_track_paths denylist (cellBrowser ucsc/allTracksHub/hub_config.json), not in a hand edit here, so the next regeneration cannot put the tracks back. Facet metadata was refreshed to match: .ra and metadata are 1:1 at 929. Subtrack priorities renumber because they are per-class sequence counters and the dropped BrainVar tracks were first in their classes. Both description pages now list their references alphabetically by first author (hg38 9 refs, mm10 7); no reference text changed. makeDoc: new section 1b documents the denylist and what is currently on it, and the counts are brought up to date. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/singleCellSignalsPeaks.ra
  • lines changed 797, context: html, text, full: html, text
    8bb883ed32e24a1007bf9f97ee1793a46bf47bd0 Thu Aug 27 10:00:43 2026 -0700
    singleCellSignalsPeaks: classify the SEA-AD and Allen tracks, add BrainVar stages 72 hg38 SEA-AD and 89 mm10 allen-basal-ganglia tracks had lost their broad cell class and were drawing in dataset colours instead of the shared palette; both assemblies are now 0 unclassified. Fix is in the hub build (cellBrowser ucsc/allTracksHub). Adds an "Other glia" class, since "Other" was doing four unrelated jobs. BrainVar goes 4 -> 13 hg38 subtracks with the new stage-split pseudobulk. Scaling moves to "autoScale group" on the composite so selected subtracks share one scale, and every bigWig now carries a data range -- without one the 13 BrainVar tracks drew as flat lines against hgTracks' built-in 0:127. Description pages and makeDocs updated, including removing the stale claim that SEA-AD is coloured by its own subclass palette. refs #37914, refs #37820 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    550a0e2666bcce27181a0cb0eab32ed261e444f6 Thu Aug 27 14:56:42 2026 -0700
    singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
  • lines changed 2, context: html, text, full: html, text
    219f66fde04ded54d6992855d1fef738aa5b6a6f Thu Aug 27 17:12:34 2026 -0700
    Give the RefSeq Historical subtrack its own dataVersion, refs #35766 The Historical track inherited the composite's dataVersion file, which tracks the current RefSeq annotation release, so the track advertised RS_2025_08 while its data is RS_2024_08. This affected three places: the long label in the browser image (simpleTracks.c appends the version for any track whose name starts with ncbiRef), the track settings page, and the details pages. A subtrack may carry its own dataVersion; trackDbSetting reads the local value first and only climbs to the parent when there isn't one. Same pattern already used by clinGenHaplo and the nmdEsc* subtracks. Also adds the version file step to the makedoc, and a reminder to the weekly notifier mail so the next refresh doesn't leave it stale again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>