Commits for hiram

v359_preview to v359_preview2 (2017-12-04 to 2017-12-11) v359

1c34cd950a1ab0e34fba3410f724b805c67704dc Mon Dec 4 11:29:39 2017 -0800

• adding all the primates refs #20216
  • src/hg/utils/phyloTrees/218way.dissect.txt - lines changed 3045, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/218wayChainNet.pl - lines changed 220, context: html, text, full: html, text

7f316821347265c823bf973b7466ad6236705cbe Tue Dec 5 11:40:11 2017 -0800

• fix uninitialized variable no redmine
  • src/hg/lib/longRange.c - lines changed 1, context: html, text, full: html, text

36ce5c7b63d028001448c971e155cff04c6317f4 Tue Dec 5 11:49:28 2017 -0800

• need parasol binaries in userApps refs #18874
  • src/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/makefile - lines changed 3, context: html, text, full: html, text

f7343a9a6a34ab63c3021c6d3353bba9b4554fdc Tue Dec 5 11:55:36 2017 -0800

• broken redirect of stderr #18874
  • src/utils/userApps/mkREADME.sh - lines changed 1, context: html, text, full: html, text

31af7965c5089fec986c85b9865604da7e6c728c Thu Dec 7 11:12:46 2017 -0800

• initial notes for theory of operation refs #18874
  • src/hg/utils/automation/openStack/README.txt - lines changed 34, context: html, text, full: html, text

b45247362a096f36ac027c459cc5bce67848b490 Thu Dec 7 16:43:13 2017 -0800

• removing strict UCSC dependencies refs #18874
  • src/hg/utils/automation/HgAutomate.pm - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/automation/doAugustus.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 20, 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/doCrispr.pl - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnpMaskSequence.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnpOrthoAlleles.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doGapOverlap.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doGenscan.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doIdKeys.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doTandemDup.pl - lines changed 5, context: html, text, full: html, text

38dae373864fe1d6bfea3155422a5ee2abe0c3ab Mon Dec 11 13:06:26 2017 -0800

• v359 preview2 refs #20654
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text