Commits for hiram

v288_preview to v288_preview2 (2013-08-07 to 2013-08-13) v288

• add note about MySQL access refs #9149
  • src/userApps/README - lines changed 17, context: html, text, full: html, text
• fixup search rule for gold track refs #8750
  • src/hg/makeDb/trackDb/gator/trackDb.ra - lines changed 5, context: html, text, full: html, text
• fixup search rule for the gold table refs #8750
  • src/hg/makeDb/doc/allMis1.txt - lines changed 25, context: html, text, full: html, text
• fixup search rule refs #9693
  • src/hg/makeDb/doc/echTel2.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra - lines changed 7, context: html, text, full: html, text
• fixup gold table search rule refs #9409
  • src/hg/makeDb/doc/oviAri3.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra - lines changed 6, context: html, text, full: html, text
• fixup search rule for gold table refs #10833
  • src/hg/makeDb/doc/vicPac2.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra - lines changed 6, context: html, text, full: html, text
• fixup gold table search rule refs #6352
  • src/hg/makeDb/doc/musFur1.txt - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• add lastz swap documentation refs #10272
  • src/hg/makeDb/doc/allMis1.txt - lines changed 24, context: html, text, full: html, text
• adding strCam1 Ostrich refs #10272
  • src/hg/utils/phyloTrees/111way.commonNames.nh - lines changed 111, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/111way.nh - lines changed 111, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/111way.scientificNames.nh - lines changed 111, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 1, context: html, text, full: html, text
• rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
  • src/hg/utils/phyloTrees/benchMark100.commonNames.nh - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.nh - lines changed 76, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.scientificNames.nh - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.sh - lines changed 2, context: html, text, full: html, text
• rearrange tree to fix lizard turtle gators and birds from 111way.nh file refs #10272
  • src/hg/utils/phyloTrees/benchMark100.sh - lines changed 2, context: html, text, full: html, text
• fixup to eliminate globals, passing data in tg structure refs #9741 #11384
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 46, context: html, text, full: html, text
• fixup function declaration format to match kent style refs #11384
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 31, context: html, text, full: html, text
• best use of slAddList refs #11384
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 4, context: html, text, full: html, text
• no trix for kids refs #8132
  • src/hg/makeDb/trackDb/makefile - lines changed 9, context: html, text, full: html, text
• source tree now functioning in new environment in hgwdev.sdsc refs #8875
  • src/hg/sqlEnvTest.sh - lines changed 6, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 1, context: html, text, full: html, text
• recognize host hgwdevSD refs #8875
  • src/hg/utils/cpAndLinkToResourceFiles.pl - lines changed 1, context: html, text, full: html, text
• eliminate useless cd WEEKLY directory changes refs #8875
  • src/utils/qa/weeklybld/makeUserApps.csh - lines changed 2, context: html, text, full: html, text
• eliminate useless cd WEEKLY directory changes refs #8875
  • src/utils/qa/weeklybld/makeStrictBeta.csh - lines changed 1, context: html, text, full: html, text
• v288 preview2
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 5, context: html, text, full: html, text