Commits for hiram

v272_preview to v272_preview2 (2012-08-14 to 2012-08-21) v272

• add special note about geoFor1
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html - lines changed 191, context: html, text, full: html, text
• update gold track frag search rule
  • src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• better regex specification to catch all frag names
  • src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra - lines changed 1, context: html, text, full: html, text
• fixup genscan table search rules
  • src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• the readonly user needs INSERT privs
  • src/product/README.mysql.setup - lines changed 3, context: html, text, full: html, text
• capture all these files from hive/data as of 15 August 2012
  • src/hg/utils/automation/ensGene/ailMel1.ensGene.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/anoCar1.ensGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/anoCar2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/bosTau3.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/bosTau4.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/bosTau6.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/calJac3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/canFam2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/canFam3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/cavPor2.ensGene.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/cavPor3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ce10.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ce6.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ce7.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ce9.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/choHof1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ci2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/cioSav2.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/danRer5.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/danRer6.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/danRer7.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/dasNov1.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/dasNov2.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/dipOrd1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/dm3.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/echTel1.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/equCab2.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/eriEur1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/felCat3.ensGene.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/felCat4.ensGene.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/fr1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/fr2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/galGal3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/gasAcu1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/gorGor1.ensGene.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/gorGor3.ensGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/hg18.ensGene.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/hg19.ensGene.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/latCha1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/loxAfr1.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/loxAfr2.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/loxAfr3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/macEug1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/melGal1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/micMur1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/mm10.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/mm8.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/mm9.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/monDom5.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/myoLuc1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/myoLuc2.ensGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/nomLeu1.ensGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ochPri2.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ornAna1.ensGene.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/oryCun1.ensGene.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/oryCun2.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/oryLat1.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/oryLat2.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/otoGar1.ensGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/panTro2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/panTro4.ensGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/ponAbe2.ensGene.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/proCap1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/pteVam1.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/rheMac2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/rn4.ensGene.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/sacCer1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/sacCer2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/sacCer3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/sorAra1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/speTri1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/speTri2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/susScr1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/susScr3.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/taeGut1.ensGene.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/tarSyr1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/tetNig1.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/tetNig2.ensGene.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/tupBel1.ensGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/turTru1.ensGene.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/vicPac1.ensGene.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/xenTro2.ensGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/ensGene/xenTro3.ensGene.ra - lines changed 3, context: html, text, full: html, text
• eliminate the difficulty with the changing structure of issue.sql by using database load and select
  • src/hg/utils/automation/grcIncidentDb.pl - lines changed 27, context: html, text, full: html, text
• bug in default BLASTZ_L value, redmine 5796 and 5882
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 1, context: html, text, full: html, text
• remove broken illegal comment
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 1, context: html, text, full: html, text
• fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
  • src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra - lines changed 9, context: html, text, full: html, text
• fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
  • src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra - lines changed 9, context: html, text, full: html, text
• fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
  • src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra - lines changed 9, context: html, text, full: html, text
• fixup search rule to avoid errors in checkHgFindSpec redmine 5727
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.ra - lines changed 15, context: html, text, full: html, text
• fixup search rule to avoid errors in checkHgFindSpec redmine 5727
  • src/hg/makeDb/trackDb/rat/rn3/trackDb.ra - lines changed 13, context: html, text, full: html, text
• update vertebrate.mod hgdownload reference
  • src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html - lines changed 1, context: html, text, full: html, text
• need full path to hgsql
  • src/hg/utils/automation/grcIncidentDb.pl - lines changed 4, context: html, text, full: html, text
• add a time result from exonNuc.fa.gz construction
  • src/hg/makeDb/doc/geoFor1.txt - lines changed 1, context: html, text, full: html, text
• fixup assembly ID
  • src/hg/makeDb/doc/mm10.txt - lines changed 3, context: html, text, full: html, text
• rerun the 4D phyloFit with the new groupings
  • src/hg/makeDb/doc/mm10.txt - lines changed 74, context: html, text, full: html, text