rhead: changes by commit

review to branch (2009-11-17 to 2009-12-01) v220

• Changed wording on description of phastCons and phyloP and trimmed references, per Adam Siepel.
  • src/hg/makeDb/trackDb/human/hg18/cons44way.html 1.13 - lines changed: 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/cons46way.html 1.4 - lines changed: 37, context: html, text, full: html, text
• Fixed broken links to WUSTL.
  • src/hg/makeDb/trackDb/worm/ce6/description.html 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/gap.html 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/gold.html 1.5 - lines changed: 1, context: html, text, full: html, text
• Trying to make the downloadsServer variable work.
  • src/hg/makeDb/trackDb/human/hg19/cons46way.html 1.5 - lines changed: 3, context: html, text, full: html, text
• downloadsServer uses personal .hg.conf, not cgi-bin/hg.conf :( :( :(
  • src/hg/makeDb/trackDb/human/hg19/cons46way.html 1.6 - lines changed: 3, context: html, text, full: html, text
• cons46way track: uncommented speciesDefaultOff line and updated assembly names for oryCun2, danRer6, and tetNig2.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.63 - lines changed: 3, context: html, text, full: html, text
• Turned on cons46way by default and changed mRNas to dense. Changed speciesCodonDefault to hg19.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.64 - lines changed: 3, context: html, text, full: html, text
• Turned of stsMap and gap by default, now that release of conservation and knownGene tracks is imminent.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.66 - lines changed: 6, context: html, text, full: html, text
• Reordered 46-way assemblies to match phylo image.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.68 - lines changed: 2, context: html, text, full: html, text
• Trying out viewLimits of -4:4 for phyloP per Adam.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.69 - lines changed: 3, context: html, text, full: html, text
• Changed viewLimits for primate phyloP to -4:1, per Hiram, based on http://genomewiki.ucsc.edu/index.php/Hg19_phyloP_histograms.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.70 - lines changed: 1, context: html, text, full: html, text