Commits for mspeir
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v501_base to v502_preview (2026-07-20 to 2026-07-27) v502
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38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
- Add singleCellSignalsPeaks track to hg38
Native faceted composite built from the per-cell-type signal (bigWig) and
peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC
datasets, re-parented under one track in the regulation group. 936 subtracks
across 9 datasets. Data files live in
/hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a
/gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build
by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py.
refs #37820
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt - lines changed 72, context: html, text, full: html, text
- src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py - lines changed 83, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html - lines changed 266, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra - lines changed 8134, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
037672a61d01d3109e8b20dff4d9142f3c8a8c66 Mon Jul 20 16:28:24 2026 -0700
- singleCellSignalsPeaks.html: reword two dataset descriptions
Recast two dangling participial phrases ("...describing about 1.2 million
elements", "...defining 359,022 elements") as plain clauses.
refs #37820
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html - lines changed 4, context: html, text, full: html, text
dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
- Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box
Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with
the current genome search box, re-recorded the step GIFs, and expanded the
guided walkthroughs (Table Browser filter/intersection and output fields,
Custom Track track line, Gateway GenArk/recent-genomes and species tree).
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/tutorials/customTrackTutorial.md - lines changed 25, context: html, text, full: html, text
- docs/tutorials/gatewayTutorial.md - lines changed 9, context: html, text, full: html, text
- docs/tutorials/tableBrowserTutorial.md - lines changed 29, context: html, text, full: html, text
- src/hg/htdocs/images/assemblySelection.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/defineRegions.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/downloadData.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/tableBrowserAnnotated.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/tableSelection.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/trackSelection.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/tutorialImages/gif/hgCustomStep1.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/tutorialImages/gif/hgCustomStep4.gif - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt1.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
fc9499685c393b53e740badf03554c65e1a0db79 Wed Jul 22 10:14:35 2026 -0700
- Fix gb101 tutorial typo and expand the blue-bar menu list
Correct the track visibility modes (dense, squish, pack, full) and add the
Downloads and View menus to the Navigating the Menus section.
refs #37355
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/tutorials/gb101.md - lines changed 4, context: html, text, full: html, text
603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
- Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
- docs/browserSlideDecks.md - lines changed 10, context: html, text, full: html, text
- docs/slideDecks/reveal.js/LICENSE - lines changed 19, context: html, text, full: html, text
- docs/slideDecks/reveal.js/dist/reveal.css - lines changed 8, context: html, text, full: html, text
- docs/slideDecks/reveal.js/dist/reveal.js - lines changed 9, context: html, text, full: html, text
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro.css - lines changed 39, context: html, text, full: html, text
- docs/slideDecks/reveal.js/dist/theme/white.css - lines changed 359, context: html, text, full: html, text
- docs/slideDecks/reveal.js/plugin/notes/notes.js - lines changed 1, context: html, text, full: html, text
- docs/slideDecks/tutorial1-basics/presentation/index.html - lines changed 35, context: html, text, full: html, text
- docs/slideDecks/tutorial1-basics/tableOfContents/index.html - lines changed 2, context: html, text, full: html, text
- docs/slideDecks/tutorial2-cancer/presentation/index.html - lines changed 22, context: html, text, full: html, text
- docs/slideDecks/tutorial3-clinical/presentation/index.html - lines changed 38, context: html, text, full: html, text
- docs/slideDecks/tutorial3-clinical/tableOfContents/index.html - lines changed 1, context: html, text, full: html, text
- docs/slideDecks/tutorial4-clinical-cases/presentation/index.html - lines changed 33, context: html, text, full: html, text
- docs/slideDecks/tutorial4-clinical-cases/tableOfContents/index.html - lines changed 9, context: html, text, full: html, text
- docs/slideDecks/tutorial5-teaching/presentation/index.html - lines changed 41, context: html, text, full: html, text
9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
- Move vendored reveal.js library out of docs/slideDecks into the source tree
Per code review feedback on #37904, the reveal.js 5.1.0 files used by the
training slide decks now live in their conventional homes rather than bundled
under docs/slideDecks/reveal.js:
- JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js),
added to that makefile; MIT LICENSE kept alongside.
- CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css),
added to that makefile.
- Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching
the existing font-awesome pattern (auto-rsynced, no makefile edit).
The white theme's @import and the five deck index.html files were updated to
reference the assets by absolute /js, /style, and /fonts paths.
refs #37904
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- docs/slideDecks/tutorial1-basics/presentation/index.html - lines changed 4, context: html, text, full: html, text
- docs/slideDecks/tutorial2-cancer/presentation/index.html - lines changed 4, context: html, text, full: html, text
- docs/slideDecks/tutorial3-clinical/presentation/index.html - lines changed 4, context: html, text, full: html, text
- docs/slideDecks/tutorial4-clinical-cases/presentation/index.html - lines changed 4, context: html, text, full: html, text
- docs/slideDecks/tutorial5-teaching/presentation/index.html - lines changed 4, context: html, text, full: html, text
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/fonts/source-sans-pro/source-sans-pro.css - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/style/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/htdocs/style/reveal-5.1.0.css - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/htdocs/style/reveal-white-5.1.0.css - lines changed 1, context: html, text, full: html, text
- src/hg/js/external/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/js/external/reveal-5.1.0.LICENSE - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/js/external/reveal-5.1.0.js - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/js/external/reveal-notes-5.1.0.js - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
b120644088d912f130ada387e34067b40616edc0 Mon Jul 27 08:19:30 2026 -0700
- minor fixes based on CR, refs #37874
- docs/browserSlideDecks.md - lines changed 1, context: html, text, full: html, text
- docs/slideDecks/tutorial5-teaching/tableOfContents/index.html - lines changed 1, context: html, text, full: html, text
57bd4d13fdfcbf7c479087eb6151a4cf2f956cbb Mon Jul 27 09:17:50 2026 -0700
- otto cron: keep cbAnnotServer gunicorn alive, refs #37492
- src/hg/utils/otto/otto.crontab - lines changed 5, context: html, text, full: html, text
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