File Changes for hiram

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• src/hg/htdocs/images/Chinchilla_lanigera.jpg
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    from Wikimedia Commons - Guerin Nicolas
• src/hg/htdocs/images/Geospiza_fortis.jpg
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    from Wikimedia Commons - Charlesjsharp
• src/hg/makeDb/doc/chiLan1.txt
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    running repeat masker and window masker
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    done with masking and cpgIslands and genscan running genbank
• src/hg/makeDb/doc/galGal4.txt
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    working on lastz to geoFor1
• src/hg/makeDb/doc/geoFor1.txt
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    initial browser build
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    running repeat masker, window masker, simple repeats, all gaps are marked
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    done with masking, starting genbank, cpgIslands and genscan
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    done with minimal set of tracks
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    default RHO position set, downloads and pushQ done, lastz swaps for melUnd1 hg19 mm10 and melGal1
• src/hg/makeDb/doc/hetGla1.txt
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    hetGla2 done and in the pushQ
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    done with liftover to hetGla2
• src/hg/makeDb/doc/hetGla2.txt
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    hetGla2 done and in the pushQ
• src/hg/makeDb/doc/hg19.txt
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    completed lastz to geoFor1
• src/hg/makeDb/doc/latCha1.txt
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    done and in the pushQ
• src/hg/makeDb/doc/melGal1.txt
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    done with lastz to geoFor1
• src/hg/makeDb/doc/melUnd1.txt
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    done and in the pushQ Redmine 6759
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    done with lastz to geoFor1
• src/hg/makeDb/doc/micMur1.txt
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    done and in the pushQ, redmine 7675
• src/hg/makeDb/doc/mm10.txt
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    done with lastz to geoFor1
• src/hg/makeDb/doc/nomLeu2.txt
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    done and in the pushQ, redmine 7676
• src/hg/makeDb/doc/ochPri2.txt
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    done and in the pushQ, redmine 7677
• src/hg/makeDb/doc/oreNil2.txt
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    done and in the pushQ, redmine 7678
• src/hg/makeDb/doc/otoGar3.txt
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    default position set at RHO and pushQ entry done
• src/hg/makeDb/doc/panTro3.txt
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    constructed liftOver to panTro4
• src/hg/makeDb/doc/panTro4.txt
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    done and in the pushQ, redmine 6356
• src/hg/makeDb/doc/papHam1.txt
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    done and in the pushQ, redmine 7669
• src/hg/makeDb/doc/proCap1.txt
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    done and in the pushQ, redmine 7680
• src/hg/makeDb/doc/pteVam1.txt
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    done and in the pushQ, redmine 7681
• src/hg/makeDb/doc/rheMac2.txt
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    liftOver constructed to rheMac3
• src/hg/makeDb/doc/rheMac3.txt
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    in the pushQ but maybe not ready to go ?
• src/hg/makeDb/doc/rn4.txt
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    liftOver to Rn5 constructed
• src/hg/makeDb/doc/saiBol1.txt
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    done and in the pushQ, redmine 6350
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    fixing date of operation
• src/hg/makeDb/doc/sorAra1.txt
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    done and in the pushQ, redmine 7682
• src/hg/makeDb/doc/speTri2.txt
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    done and in the pushQ, redmine 7319
• src/hg/makeDb/doc/susScr2.txt
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    liftOver to susScr3 done
• src/hg/makeDb/doc/susScr3.txt
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    done and in the pushQ, redmine 4015
• src/hg/makeDb/doc/taeGut1.txt
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    working on lastz to geoFor1
• src/hg/makeDb/doc/tarSyr1.txt
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    done and in the pushQ, redmine 7683
• src/hg/makeDb/doc/triMan1.txt
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    done and in the pushQ, redmine 7684
• src/hg/makeDb/doc/tupBel1.txt
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    done and in the pushQ, redmine 7684
• src/hg/makeDb/doc/turTru2.txt
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    done and in the pushQ, redmine 7686
• src/hg/makeDb/doc/vicPac1.txt
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    setting default track visibilities
• src/hg/makeDb/genbank/etc/align.dbs
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    Added geoFor1.
• src/hg/makeDb/genbank/etc/genbank.conf
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    adding geoFor1 medium ground finch
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    adding chiLan1 Chinchilla
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    Added geoFor1.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    adding definition for geoForNames
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    adding definition for chiLanNames
• src/hg/makeDb/schema/all.joiner
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    adding geoFor1 Medium Ground Finch rules
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    adding geoFor1 to the chain/net list
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/birds/geoFor1/description.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/geoFor1/gap.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/geoFor1/gold.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chinchilla/chiLan1/gap.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chinchilla/chiLan1/gold.html
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chinchilla/chiLan1/trackDb.ra
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    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/makefile
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    adding geoFor1 to the build
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    adding Chinchilla to the build
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
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    setting default visibilities
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
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    seting default track visibilities
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
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    setting default visibilities for tracks
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
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    adding override for PanTro4
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
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    set default track visibilities
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
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    setting default track visibilities
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    adding definition for chainNetPanTro4
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    adding melUnd1 and geoFor1
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
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    setting default track visibilities
• src/hg/utils/automation/makeDownloads.pl
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    adding genbank usage message
• src/hg/utils/phyloTrees/placentals.txt
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    add medium ground finch geoFor1 and Chinchilla lanigera chiLan
• src/hg/utils/phyloTrees/vertebrates.txt
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    add medium ground finch geoFor1 and Chinchilla lanigera chiLan