File Changes for hiram

v304_base to v305_preview (2014-08-11 to 2014-08-18) v305

• src/hg/lib/chromInfo.sql
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    allow maximum length for mirror site builds refs #13792
• src/hg/makeDb/doc/hg38.txt
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    building genomicSuperDups track refs #13580
• src/hg/makeDb/schema/all.joiner
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    tables ignored centromeres for hg38 refs #12689
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
  • lines changed 80, context: html, text, full: html, text
    trying visibility settings refs #13713
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
  • lines changed 31, context: html, text, full: html, text
    adding methods and credits sections refs #12689
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    override for genomicSuperDups to get them into the rep group refs #13580
• src/hg/utils/automation/doRepeatMasker.pl
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    allow loading of a different named table refs #9741
• src/hg/utils/automation/fetchOneNcbi.sh
  • lines changed 34, context: html, text, full: html, text
    operating the rsync to fetch a new assembly refs #252
• src/hg/utils/automation/quickDbBuild.sh
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    simple database and dbDb builds for a database refs #252
• src/hg/utils/automation/quickDbdbBuild.sh
  • lines changed 115, context: html, text, full: html, text
    simple database and dbDb builds for a database refs #252
• src/hg/utils/automation/unplacedScaffolds.pl
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    now with -mito argument to add chrM sequence from genbank id refs #272
• src/hg/utils/phyloTrees/120way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/122way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/123way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/126way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/129way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/130way.scientificNames.nh
  • lines changed 2, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/131way.scientificNames.nh
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    correcting a few names refs #10272
• src/hg/utils/phyloTrees/166way.commonNames.nh
  • lines changed 8, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/166way.scientificNames.nh
  • lines changed 2, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/171way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/171way.scientificNames.nh
  • lines changed 2, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/172way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/172way.scientificNames.nh
  • lines changed 2, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/174way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    correcting a few names refs #10272
• src/hg/utils/phyloTrees/181way.commonNames.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/181way.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/181way.scientificNames.nh
  • lines changed 181, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 15, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/db.ncbiTaxId.tab
  • lines changed 9, context: html, text, full: html, text
    adding new assemblies bosTau bucRhi chaVoc cypVar esoLuc halLeu manVit notCor tinGut refs #11636
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    adding new orgs corCor manPen refs #11636
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 15, context: html, text, full: html, text
    adding new orgs hg38 bosTau8 manPen1 chaVoc2 bucRhi1 tinGut2 halLeu1 corCor1 manVit2 phaCar1 croPor0 gavGan0 notCor cypVar1 esoLuc1 refs #11636
  • lines changed 1, context: html, text, full: html, text
    fixup notCor name refs #11636
  • lines changed 1, context: html, text, full: html, text
    add order key for manPen1 refs #11636
• src/hg/utils/phyloTrees/makefile
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    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 6, context: html, text, full: html, text
    adding galVar Malayan flying lemur and phyCat sperm whale - Physeter catodon refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 11, context: html, text, full: html, text
    adding bucRhe1 corCor1 cypVar1 esoLuc1 halLeu1 manPen1 notCor1 refs #10272
• src/hg/utils/phyloTrees/speciesList.sh
  • lines changed 2, context: html, text, full: html, text
    fixup tricky name mangling refs #10272
• src/utils/qa/weeklybld/buildEnv.csh
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    v305 preview1 refs #13703