Commits for katrina

v250_preview to v250_preview2 (2011-04-05 to 2011-04-12) v250

• edits to fileSearch doc and trying a different template. Having trouble getting topbar to display
  • src/hg/htdocs/goldenPath/help/fileSearch.html - lines changed 93, context: html, text, full: html, text
• Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeMapability.ra - lines changed 162, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriBip.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeMapability.ra - lines changed 162, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriBip.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra - lines changed 12, context: html, text, full: html, text
• making executable so that the server side include (for the topbar) will work
  • src/hg/htdocs/goldenPath/help/fileSearch.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• making changes suggested by Vanessa
  • src/hg/htdocs/goldenPath/help/fileSearch.html - lines changed 4, context: html, text, full: html, text
• fixed a repeated word
  • src/hg/htdocs/goldenPath/help/fileSearch.html - lines changed 1, context: html, text, full: html, text
• changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriNRE.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriNRE.ra - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 44, context: html, text, full: html, text
• changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlShortRnaSeq.ra - lines changed 1018, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra - lines changed 44, context: html, text, full: html, text
• changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisDnaPet.ra - lines changed 551, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra - lines changed 7, context: html, text, full: html, text
• putting wgEncodeHudsonalphaMethylSeq in its own .ra and .new.ra file instead of having them in the trackDb.wgEncode.ra file; note there was already a .ra file, but it wasn't being used, so I just wrote over it.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 736, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.new.ra - lines changed 324, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra - lines changed 33, context: html, text, full: html, text
• changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaMethylSeq.ra - lines changed 1612, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaMethylSeq.ra - lines changed 1612, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• forgot to copy the wgEncodeHudsonalphaMehthylSeq.new.ra over the wgEncodeHudsonalphaMethylSeq.ra; doing that now which finalizes switch to use of metaDb be removing trackDb metadata lines, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra - lines changed 29, context: html, text, full: html, text
• switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeDukeAffyExonArray.ra - lines changed 1045, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra - lines changed 59, context: html, text, full: html, text
• switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHelicosRnaSeq.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra - lines changed 4, context: html, text, full: html, text
• switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeAffyRnaChip.ra - lines changed 1873, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra - lines changed 104, context: html, text, full: html, text
• switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisRnaSeq.ra - lines changed 439, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra - lines changed 18, context: html, text, full: html, text
• changed order of 'normal' items in list of colors
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html - lines changed 2, context: html, text, full: html, text
• adding release notes section to the description of the hg18 Common cell cnv, redmine 3499
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html - lines changed 6, context: html, text, full: html, text
• staging Common Cell CNV (Release 2) on beta
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaCnv.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• releasing Common Cell CNV (Release 2) to the RR, redmine #3499
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaCnv.ra - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra - lines changed 9, context: html, text, full: html, text