File Changes for hiram

v289_preview2 to v289_base (2013-09-02 to 2013-09-09) v289

• src/hg/inc/versionInfo.h
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    New version number v289
• src/hg/makeDb/doc/hg19.txt
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    starting lastz for neoBri1 hapBur1 punNye1 astMex1 lepOcu1 refs #10272
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    wrapping up lastz runs for gadMor1 chrPic1 myoLuc2 chiLan1 pelSin1 mesAur1 myoDav1 eptFus1 takFla1 refs #10272
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    starting lastz run on allSin1 refs #10272
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    wrapping up lastz runs for gadMor1 mesAur1 pteAle1 myoDav1 eptFus1 takFla1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 allSin1 refs #10272
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    finishing up lastz runs for criGri1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 mayZeb1 refs #10272
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    done with lastz for criGri1 pteAle1 mayZeb1 refs #10272
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    restarting lastz run on allSin1 to fix chrM missing refs #10272
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    finishing up allSin1 lastz run refs #10272
• src/hg/utils/automation/EnsGeneAutomate.pm
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    Ensembl v73 update and their FTP server has changed its output refs #11675
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    fixup a couple of broken names refs #11675
• src/hg/utils/automation/findEnsFtpNames.sh
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    Ensembl v73 update and their FTP server has changed its output refs #11675
• src/hg/utils/phyloTrees/112way.commonNames.nh
  • lines changed 112, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/112way.nh
  • lines changed 111, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/112way.scientificNames.nh
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
  • lines changed 15, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
  • lines changed 15, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.sh
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/makefile
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 14, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
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    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/userApps/Makefile
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    correct testing for existence of downloaded source refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
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    v289 final build