Commits for hiram

v313_preview to v313_preview2 (2015-02-23 to 2015-03-02) v313

• can not echo to /dev/stderr from within a cron job use bash redirect instead refs #14821
  
  • src/utils/qa/weeklybld/buildWithUseCases - lines changed 2, context: html, text, full: html, text
• use bash redirection instead of /dev/stderr in case of cron job operations refs #14821
  
  • src/utils/gitTools/gilt - lines changed 3, context: html, text, full: html, text
  • src/utils/gitTools/gitFiles - lines changed 3, context: html, text, full: html, text
• correcting make beta to be in src/ instead of just src/hg/ refs #14768
  
  • src/utils/qa/weeklybld/buildBeta.csh - lines changed 3, context: html, text, full: html, text
• add search rule for gold table refs #14410
  
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra - lines changed 6, context: html, text, full: html, text
• add search rule for gold table refs #14410
  
  • src/hg/makeDb/doc/tarSyr2/initialBuild.txt - lines changed 28, context: html, text, full: html, text
• adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
  
  • src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.chainNet.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.chainNet.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.chainNet.ra - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/trackDb.ncbiGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.chainNet.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra - lines changed 110, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.chainNet.ra - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.chainNet.ra - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.chainNet.ra - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.chainNet.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• correcting long standing error in otherDb MicMur1 instead of otherDb micMur1 refs #14410
  
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
• added search rule for hg38 patch2 names refs #14167
  
  • src/hg/makeDb/trackDb/human/hg38/hg38Patch2.ra - lines changed 8, context: html, text, full: html, text
• done with the rework of this with the correct rhiRox1 sequence refs #14410
  
  • src/hg/makeDb/doc/tarSyr2/multiz17way.txt - lines changed 244, context: html, text, full: html, text
• rerun rhiRox1 with correct sequence refs #14560
  
  • src/hg/makeDb/doc/tarSyr2/lastzRuns.txt - lines changed 23, context: html, text, full: html, text
• v313 preview2 refs #14887
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text