Commits for hiram

v288_base to v289_preview (2013-08-19 to 2013-08-26) v289

• adding -lstdc++ and -lrt to all MYSQLLIBS in case of MySQL v5.6 refs #9149
  • src/inc/common.mk - lines changed 3, context: html, text, full: html, text
• running lastz for fr3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 67, context: html, text, full: html, text
• some kind of merge is taking place, I don't know what it is.
• done with fr3 lastz refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 14, context: html, text, full: html, text
• Some kind of merge is taking place for some reason.
• moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
  • src/hg/utils/automation/HgAutomate.pm - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doGenscan.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doHgNearBlastp.pl - lines changed 4, context: html, text, full: html, text
• fixup reference to hgcentraltest as localhost instead of genome-testdb refs #8875
  • src/hg/utils/automation/HgAutomate.pm - lines changed 1, context: html, text, full: html, text
• merging something
• fixup use of ku kluster for options to engines for RM refs #8875
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 5, context: html, text, full: html, text
• starting lipVex1 lastz refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 63, context: html, text, full: html, text
• always merging something
• using sendmail instead of mail because this mail is different than before refs #8875
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 8, context: html, text, full: html, text
• some kind of merge happening
• adding steve to the notification email refs #8875
  • src/utils/qa/weeklybld/doHgTablesTestRobot.csh - lines changed 2, context: html, text, full: html, text
• adding lipVex and myoBri Brandt's Myotis (bat) - Myotis brandtii and Yangtze River Dolphin Lipotes vexillifer refs @10272
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 7, context: html, text, full: html, text
• adding ucscToINSDC track refs #11348
  • src/hg/makeDb/doc/ailMel1.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/bosTau7.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/calJac3.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/canFam3.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 13, context: html, text, full: html, text
• some kind of merge happening
• adding ucscToINSDC checking refs #11348
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text
• merging something
• correct overrides for chain net settings on hg19 vs. allMis1 refs #8750
  • src/hg/makeDb/trackDb/gator/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gator/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra - lines changed 7, context: html, text, full: html, text
• something is merging during a pull
• adding ucscToINSDC track refs #11348
  • src/hg/makeDb/doc/cavPor3.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/cerSim1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/chrPic1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer7.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/dasNov3.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/felCat5.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/fr3.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/gadMor1.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/galGal4.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/hetGla2.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/latCha1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/loxAfr3.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/macEug2.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/melGal1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/melUnd1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/musFur1.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/myoLuc2.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/oreNil2.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/oryCun2.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/otoGar3.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/petMar2.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/rheMac3.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/rn5.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/saiBol1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/sarHar1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/speTri2.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/triMan1.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/turTru2.txt - lines changed 19, context: html, text, full: html, text
• v289 preview1
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text
• some kind of merge is happening