mikep: changes by commit

branch to review (2009-06-23 to 2009-06-30) v209

• GIS RnaSeq base coloring
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.375 - lines changed: 13, context: html, text, full: html, text
• adding hg libs for user apps
  • src/makefile 1.61 - lines changed: 1, context: html, text, full: html, text
• liftover is part of larger suite of user apps now
  • src/utils/qa/weeklybld/makeLiftOver.csh 1.2 - lines changed: 141, context: html, text, full: html, text
  • src/utils/qa/weeklybld/makeUserApps.csh 1.1 - lines changed: 47, context: html, text, full: html, text
• new process for copying userApps binaries (not just liftOver now)
  • src/utils/qa/weeklybld/doHgDownloadUtils.csh 1.5 - lines changed: 16, context: html, text, full: html, text
  • src/utils/qa/weeklybld/makeUserApps.csh 1.2 - lines changed: 20, context: html, text, full: html, text
• Track documentation for GIS RNA-seq
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html 1.1 - lines changed: 102, context: html, text, full: html, text
• format tweak
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html 1.2 - lines changed: 7, context: html, text, full: html, text
• updated version of dna-pet doco
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html 1.3 - lines changed: 78, context: html, text, full: html, text
• added data-release policy dna-pet doco
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html 1.4 - lines changed: 9, context: html, text, full: html, text
• tweak to UI
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.380 - lines changed: 1, context: html, text, full: html, text
• new clone-free method for GIS RNA-PET
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html 1.6 - lines changed: 74, context: html, text, full: html, text
• added split tags, and raw data for Solexa
  • src/hg/encode/DAFs/GisRnaSeq.daf 1.4 - lines changed: 17, context: html, text, full: html, text
• temporary new version until we get CSHL working with bigBed tagAlign
  • src/hg/encode/DAFs/CshlRnaSeq.daf 1.4 - lines changed: 8, context: html, text, full: html, text
• loading CSHL bigbed tagAligns
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.384 - lines changed: 234, context: html, text, full: html, text