Commits for mspeir

v345_preview2 to v345_base (2017-02-13 to 2017-02-20) v345

52e3b3f711c7a7e53fc50c1f9d1d82c2ba2f729d Tue Feb 14 11:09:29 2017 -0800

• Adding data access section to track desc. page. Other minor desc. page edits for consistency and clarification. Changed color of ncbiRefSeqPsl track to black. Turned off UCSC RefSeq track by default and turned on RefSeq Curated per Jim's feedback. refs #13673
  • src/hg/makeDb/trackDb/refSeqComposite.html - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 4, context: html, text, full: html, text

e4cf75bb701b40a808bc07fc23e1cd66049c6533 Tue Feb 14 12:36:10 2017 -0800

• Adding canPack setting to all transmap v4 track, refs #18818
  • src/hg/makeDb/trackDb/trackDb.transMap.ra - lines changed 4, context: html, text, full: html, text

cddaecf4812321f3bdc70341a86d82cf0ac26da9 Wed Feb 15 09:28:15 2017 -0800

• Adding new big* types to factory.py. Changed how pslQa.py creates itemSizes and chromSizes files. Uses built-in tempfile functions to create so they are automatically cleaned up on program close. no redmine
  • python/lib/ucscGb/qa/tables/factory.py - lines changed 2, context: html, text, full: html, text
  • python/lib/ucscGb/qa/tables/pslQa.py - lines changed 14, context: html, text, full: html, text

36a49772a10673662471b7b1edc2e1744006a466 Wed Feb 15 09:48:59 2017 -0800

• Tweaking usage message to mention runBits.csh. Adding main function to qaGbTracks. no redmine
  • src/utils/qa/qaGbTracks - lines changed 9, context: html, text, full: html, text

3a9ce6d9d2d72ce6acc98787076570c6b24edf0d Fri Feb 17 12:53:50 2017 -0800

• Changing links to old genomics institute site to new site, refs #14220
  • src/hg/htdocs/Neandertal/index.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbFooter.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/inc/gbsFooter.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/inc/globalNavBar.inc - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/jWestFooter.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/index.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/staff.html - lines changed 2, context: html, text, full: html, text

9372c4f00b7fa32ac3a33e9003f498b352099373 Fri Feb 17 12:56:32 2017 -0800

• Changing links to old genomics institute site to new site for track description pages, refs #14220
  • src/hg/makeDb/trackDb/human/hg17/encodeMavidCons.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMavidElements.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMlaganCons.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMlaganElements.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeTbaCons.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html - lines changed 1, context: html, text, full: html, text

c7b6c05576f076b0a230d8b31d00fec194aab3ea Fri Feb 17 13:13:17 2017 -0800

• Adding back some removed text based on CR, refs #18564 #7380
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 8, context: html, text, full: html, text

6140d595a303099155ac6f518feef66fdcd4211b Fri Feb 17 13:18:40 2017 -0800

• Adding mention of hgsql and hgsqldump to mysql details page, refs #9058
  • src/hg/htdocs/goldenPath/help/mysql.html - lines changed 22, context: html, text, full: html, text

7d7c9d75a7e31d4acb3ae704e377e8727a058a4f Fri Feb 17 13:48:57 2017 -0800

• Adding also to sentence, no redmine
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 1, context: html, text, full: html, text

4eec29fffd298603f97760e657f686ecfb640009 Fri Feb 17 14:40:36 2017 -0800

• Correcting mistake in ncbiRefSeqCurated search rule, refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

90ebbccbe1b8a99fac85f27a51a70c6a9a54d3fb Fri Feb 17 14:53:59 2017 -0800

• Removing mention of hgsqldump as it doesn't work with the public mysql server, refs #9058
  • src/hg/htdocs/goldenPath/help/mysql.html - lines changed 10, context: html, text, full: html, text