Commits for max

v337_preview to v337_preview2 (2016-08-01 to 2016-08-08) v337

c5cba6f47e775308f8d2ef9303857423ff9f6561 Mon Aug 1 14:23:34 2016 -0700

• adding tool to create CIRM CDW summary page. It creates a plot with cells placed on a 2D-space, so similar cells are located close together (T-SNE dimensionality reduction, Seurat package). This a python command line tool that creates R scripts and finally outputs a static html page with lots of D3 javascript in it. An unusual architecture, but I did not find a better solution that is compatible with our security constraints in the CIRM project
  
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 1939, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwSummary/makefile - lines changed 9, context: html, text, full: html, text

de1276834030ebf345be51b4c7d1f1008c10684d Mon Aug 1 15:28:43 2016 -0700

• for the CIRM CDW, make the download button put files into the appropriate subdirectories, creating them on the way
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 43, context: html, text, full: html, text

f96ae7c4d8f747d1eba8728c2263870f0f6d2c16 Mon Aug 1 15:40:09 2016 -0700

• make sure that CDW CIRM download all button does not write into unexpected directories
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 12, context: html, text, full: html, text

df83ccb73d649fdc14703e3b7cb7081845ce2085 Mon Aug 1 16:09:09 2016 -0700

• adding multithreading to the CIRM CDW new download option
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text

b333eb9809c523502a638a910e17abc47e2c2d09 Wed Aug 3 07:09:48 2016 -0700

• again trying to fix an issue with handling of ${, $}, refs #17785, #15480
  
  • src/hg/lib/hui.c - lines changed 7, context: html, text, full: html, text

7cf81f9887e699b4177d3bbdfd59b719e80f3c07 Wed Aug 3 07:16:31 2016 -0700

• trying to improve documentation of special variables in urls, refs #17785
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 8, context: html, text, full: html, text

8cb0eb5850ff9883a1a278c1607998f0a6046bcb Thu Aug 4 08:56:32 2016 -0700

• adding internal ability to draw multiple highlights.
  refs #14951. There is no way to set these currently in the UI,
  as this would be a whole project of its own. Also, in multi-exon
  mode, it will only draw the first region, if multiple ones are defined.
  
  • src/hg/hgTracks/hgTracks.c - lines changed 29, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 9, context: html, text, full: html, text

493e6392ace2fe0653519c2753e3d81622d0ee1a Fri Aug 5 09:22:46 2016 -0700

• cosmetic changes in cdwSummary, no redmine
  
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 7, context: html, text, full: html, text

714c83fd8a7fe394d6f9767b5ebce77f37846cb8 Fri Aug 5 11:10:32 2016 -0700

• small change to browser installer hg.conf to show that http-only is possible
  
  • src/product/installer/browserSetup.sh - lines changed 3, context: html, text, full: html, text

bd8c3d3124817d7ec82a33b9f27a9a9d56df8ef4 Fri Aug 5 14:24:37 2016 -0700

• hotkey fix, refs #17844
  
  • src/hg/hgTracks/hgTracks.c - lines changed 6, context: html, text, full: html, text

102acb1e520a68eed9cca59f1a39a0cfc3de84ab Fri Aug 5 14:57:31 2016 -0700

• fixing gbib speed problem after refseq change, refs #17842
  
  • src/browserbox/root/updateBrowser.sh - lines changed 7, context: html, text, full: html, text