File Changes for hiram

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

• src/hg/makeDb/doc/geoFor1.txt
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    add a time result from exonNuc.fa.gz construction
• src/hg/makeDb/doc/mm10.txt
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    fixup assembly ID
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    rerun the 4D phyloFit with the new groupings
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    update vertebrate.mod hgdownload reference
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
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    update gold track frag search rule
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    better regex specification to catch all frag names
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    add special note about geoFor1
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
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    add special note about geoFor1
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
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    update gold track frag search rule
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    better regex specification to catch all frag names
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    fixup genscan table search rules
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
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    fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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    update gold track frag search rule
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    better regex specification to catch all frag names
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    fixup genscan table search rules
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
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    fixup search rule to avoid errors in checkHgFindSpec redmine 5727
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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    fixup search rule to avoid errors in checkHgFindSpec redmine 5727
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
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    update gold track frag search rule
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    better regex specification to catch all frag names
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    fixup genscan table search rules
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
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    fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra
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    update gold track frag search rule
• src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
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    fixup ensGen protein search rule to avoid errors in checkHgFindSpec redmine 5727
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
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    update gold track frag search rule
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    better regex specification to catch all frag names
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    fixup genscan table search rules
• src/hg/utils/automation/EnsGeneAutomate.pm
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    remove broken illegal comment
• src/hg/utils/automation/doBlastzChainNet.pl
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    bug in default BLASTZ_L value, redmine 5796 and 5882
• src/hg/utils/automation/ensGene/ailMel1.ensGene.ra
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• src/hg/utils/automation/ensGene/anoCar1.ensGene.ra
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• src/hg/utils/automation/ensGene/anoCar2.ensGene.ra
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• src/hg/utils/automation/ensGene/bosTau3.ensGene.ra
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• src/hg/utils/automation/ensGene/bosTau4.ensGene.ra
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• src/hg/utils/automation/ensGene/bosTau6.ensGene.ra
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• src/hg/utils/automation/ensGene/calJac3.ensGene.ra
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• src/hg/utils/automation/ensGene/canFam2.ensGene.ra
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• src/hg/utils/automation/ensGene/canFam3.ensGene.ra
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• src/hg/utils/automation/ensGene/cavPor2.ensGene.ra
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• src/hg/utils/automation/ensGene/cavPor3.ensGene.ra
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• src/hg/utils/automation/ensGene/ce10.ensGene.ra
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• src/hg/utils/automation/ensGene/ce6.ensGene.ra
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• src/hg/utils/automation/ensGene/ce7.ensGene.ra
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• src/hg/utils/automation/ensGene/ce9.ensGene.ra
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• src/hg/utils/automation/ensGene/choHof1.ensGene.ra
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• src/hg/utils/automation/ensGene/ci2.ensGene.ra
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• src/hg/utils/automation/ensGene/cioSav2.ensGene.ra
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• src/hg/utils/automation/ensGene/danRer5.ensGene.ra
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• src/hg/utils/automation/ensGene/danRer6.ensGene.ra
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• src/hg/utils/automation/ensGene/danRer7.ensGene.ra
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• src/hg/utils/automation/ensGene/dasNov1.ensGene.ra
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• src/hg/utils/automation/ensGene/dasNov2.ensGene.ra
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• src/hg/utils/automation/ensGene/dipOrd1.ensGene.ra
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• src/hg/utils/automation/ensGene/dm3.ensGene.ra
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• src/hg/utils/automation/grcIncidentDb.pl
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    eliminate the difficulty with the changing structure of issue.sql by using database load and select
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    need full path to hgsql
• src/product/README.mysql.setup
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    the readonly user needs INSERT privs