File Changes for hiram

v267_preview2 to v267_base (2012-05-08 to 2012-05-15) v267

• src/hg/htdocs/images/Canis_lupus_familiaris.jpg
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    dog also has this scientific name
• src/hg/makeDb/doc/chrPic1.txt
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    completed genbank run
• src/hg/makeDb/doc/dasNov3.txt
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    done with genbank run
• src/hg/makeDb/doc/dipOrd1.txt
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    done with genbank run
• src/hg/makeDb/doc/felCat5.txt
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    done with genbank run
• src/hg/makeDb/doc/galGal4.txt
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    done with genbank run
• src/hg/makeDb/doc/hetGla2.txt
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    done with genbank run
• src/hg/makeDb/doc/hg19.txt
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    lifting HapMap recombination maps from hg18
• src/hg/makeDb/doc/latCha1.txt
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    done with genbank run
• src/hg/makeDb/doc/mm10.txt
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    liftover to mm9
• src/hg/makeDb/doc/nomLeu2.txt
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    done with genbank run
• src/hg/makeDb/doc/otoGar3.txt
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    done with genbank run
• src/hg/makeDb/doc/rn5.txt
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    genbank done
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    download files constructed, ready for documentation
• src/hg/makeDb/doc/saiBol1.txt
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    done with genbank run
• src/hg/makeDb/doc/susScr3.txt
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    done with genbank run
• src/hg/makeDb/genbank/etc/align.dbs
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    Added rn5.
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    Added galGal4.
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    Added felCat5.
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    Added susScr3.
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    Added chrPic1.
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    Added dasNov3.
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    Added dipOrd1.
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    Added hetGla2.
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    Added otoGar3.
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    Added nomLeu2.
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    Added saiBol1.
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    Added latCha1.
• src/hg/makeDb/genbank/etc/genbank.conf
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    adding eriEur1 European hedgehog
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    adding gadMor1 Atlantic cod
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    adding latCha1 Coelacanth
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    adding melUnd1 budgerigar
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    adding micMur1 mouse lemur
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    adding ochPri2 pika
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    adding oreNil2 Nile tilapia
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    adding proCap1 Rock hyrax
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    adding pteVam1 megabat
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    adding saiBol1 squirrel monkey
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    adding sorAra1 common shrew
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    adding speTri2 13-lined ground squirrel
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    adding tarSyr1 tarsier
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    adding tupBel1 tree shrew
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    adding vicPac1 alpaca
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    Added rn5.
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    Added galGal4.
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    Added felCat5.
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    Added susScr3.
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    Added chrPic1.
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    Added dasNov3.
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    Added dipOrd1.
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    Added hetGla2.
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    Added otoGar3.
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    Added nomLeu2.
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    Added saiBol1.
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    Added latCha1.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    adding: otoGar turTru eriEur gadMor latCha melUnd micMur ochPri oreNil proCap pteVam saiBol sorAra speTri tarSyr tupBel vicPac
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    additional name for Saimiri boliviensis
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    speTri AKA Ictidomys tridecemlineatus
• src/hg/makeDb/schema/all.joiner
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    add ignore tables for the ones in decodeRmap
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    adding rn5 and chain net Mm10 definitions
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    adding assemblies: canFam3,chrPic1,dasNov3,felCat5,gadMor1,galGal4,hetGla2,latCha1,melUnd1,nomLeu2,oreNil2,otoGar3,panTro4,papHam1,saiBol1,speTri2,susScr3,triMan1,turTru2
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    fixup missing tables in the new databases just added
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    clean up all errors on the new assemblies recently added
• src/hg/makeDb/trackDb/dog/canFam3/description.html
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    new style minimalist content
• src/hg/makeDb/trackDb/rat/rn5/description.html
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    new style minimalist content
• src/hg/utils/automation/doBlastzChainNet.pl
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    default smallClusterHub is encodek, memk is gone
• src/hg/utils/automation/doWindowMasker.pl
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    name of doLoad step script is actually doLoad
• src/product/README.trackDb
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    correct reference to trackDb/README file