File Changes for hiram

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

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