Commits for hiram

v289_preview2 to v289_base (2013-09-02 to 2013-09-09) v289

• correct testing for existence of downloaded source refs #9149
  • src/userApps/Makefile - lines changed 1, context: html, text, full: html, text
• starting lastz for neoBri1 hapBur1 punNye1 astMex1 lepOcu1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 310, context: html, text, full: html, text
• wrapping up lastz runs for gadMor1 chrPic1 myoLuc2 chiLan1 pelSin1 mesAur1 myoDav1 eptFus1 takFla1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 46, context: html, text, full: html, text
• starting lastz run on allSin1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 71, context: html, text, full: html, text
• wrapping up lastz runs for gadMor1 mesAur1 pteAle1 myoDav1 eptFus1 takFla1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 allSin1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 56, context: html, text, full: html, text
• finishing up lastz runs for criGri1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 mayZeb1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 99, context: html, text, full: html, text
• done with lastz for criGri1 pteAle1 mayZeb1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 17, context: html, text, full: html, text
• restarting lastz run on allSin1 to fix chrM missing refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
• Ensembl v73 update and their FTP server has changed its output refs #11675
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 203, context: html, text, full: html, text
  • src/hg/utils/automation/findEnsFtpNames.sh - lines changed 15, context: html, text, full: html, text
• fixup a couple of broken names refs #11675
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 4, context: html, text, full: html, text
• adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
  • src/hg/utils/phyloTrees/112way.commonNames.nh - lines changed 112, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/112way.nh - lines changed 111, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/112way.scientificNames.nh - lines changed 112, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 2, 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
• adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
  • src/hg/utils/phyloTrees/benchMark100.commonNames.nh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.nh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.scientificNames.nh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 3, context: html, text, full: html, text
• finishing up allSin1 lastz run refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 13, context: html, text, full: html, text
• v289 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v289
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text