Commits for steve

v266_base to v267_preview (2012-04-24 to 2012-05-01) v267

• Added new 'Publications' section with specified citations (redmine #7514)
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html - lines changed 82, context: html, text, full: html, text
• Added new 'Publications' section with specified citations (redmine #7514)
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html - lines changed 15, context: html, text, full: html, text
• Staging Caltech RNA-Seq (Release 1) on beta (redmine #4156)
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechRnaSeq.ra - lines changed 577, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Staging RIKEN CAGE Loc (Release 3) on beta (redmine #6579)
  • src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra - lines changed 10195, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• Added new menu bar file that includes a link to Software Tools (redmine #7701)
  • src/hg/htdocs/inc/encodeProjectSoftware.topbar.html - lines changed 38, context: html, text, full: html, text
• Added a dash between 'Data Standards' and 'Software Tools' (redmine #7701)
  • src/hg/htdocs/inc/encodeProjectSoftware.topbar.html - lines changed 1, context: html, text, full: html, text
• Put tools into categories and alphabetized per Kate's request (redmine #7701)
  • src/hg/htdocs/ENCODE/analysisTools.html - lines changed 64, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/encodeTools.html - lines changed 178, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/softwareTools.html - lines changed 2, context: html, text, full: html, text
• Corrected spelling of RSEQtools (redmine #7701)
  • src/hg/htdocs/ENCODE/encodeTools.html - lines changed 1, context: html, text, full: html, text
• Made change suggested by Katrina in code review (redmine #7738 note 4)
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
  • src/hg/makeDb/trackDb/transMap.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnMRna.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnRefSeq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnSplicedEst.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/transMapAlnUcscGenes.html - lines changed 3, context: html, text, full: html, text
• Made changes suggested by Katrina in code review (redmine #7738 note 8)
  • src/hg/htdocs/ENCODE/encodeTools.html - lines changed 13, context: html, text, full: html, text
• Fixed broken link
  • src/hg/makeDb/trackDb/mouse/ikmc.html - lines changed 1, context: html, text, full: html, text
• Ruihua added freeze date to one entry (redmine #4156)
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• Venkat fixed peak file (redmine #6703)
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra - lines changed 3, context: html, text, full: html, text
• Releasing PSU Histone (Release 1) to RR (redmine #111)
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuHistone.ra - lines changed 8044, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Added line for PSU Histone (redmine #111)
  • src/hg/htdocs/ENCODE/downloadsMouse.html - lines changed 4, context: html, text, full: html, text
• Made changes suggested by Katrina in code review (redmine #7738)
  • src/hg/htdocs/ENCODE/analysisTools.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/encodeTools.html - lines changed 34, context: html, text, full: html, text