File Changes for hiram

v276_preview to v276_preview2 (2012-11-06 to 2012-11-13) v276

• src/hg/htdocs/images/phylo/petMar2_7way.png
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    7-way tree image for Lamprey
• src/hg/lib/trackDbCustom.c
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    add bedTail to the allowed composite configuration options, same as bed types
• src/hg/makeDb/doc/braFlo2.txt
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    add note about Nature paper and 11.5X coverage
• src/hg/makeDb/doc/equCab2.txt
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    running white rhino lastz
• src/hg/makeDb/doc/hg19.txt
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    COSMIC v61 update done redmine 9386, and liftOver to hg17, redmine 9571
• src/hg/makeDb/doc/mm10Strains1.txt
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    completed lastz alignment to mm10
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    change table name from mm10Strains1LiftOverPsl to altSeqLiftOverPslStrains1 to help hgc display the sequence
• src/hg/makeDb/doc/petMar2.txt
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    download files constructed for the 7-way alignment
• src/hg/makeDb/trackDb/chainNetPetMar1.ra
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    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/chainNetPetMar2.ra
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    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
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    remove extra . following May.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
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    credit BCM with Broad
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    add BCM to NCBI assembly information
• src/hg/makeDb/trackDb/makefile
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    papAnu2 is the same identity as papHam1
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
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    add release tag to override block in medaka petMar1
• src/hg/makeDb/trackDb/mouse/mm10/chain.petMar1.ra
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    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/chain.petMar2.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1Composite.ra
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    the alternate strains mapping to the reference, redmine 7341
• src/hg/makeDb/trackDb/mouse/mm10/net.petMar1.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/net.petMar2.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    adding the strains composite track to mm10 and the mm10Locations track to mm10Strains1
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10Strains1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding the strains composite track to mm10 and the mm10Locations track to mm10Strains1
• src/hg/makeDb/trackDb/tagTypes.tab
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    add bedTail to the allowed composite configuration options, same as bed types
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 100, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
  • lines changed 1, context: html, text, full: html, text
    add release tag to override block in medaka petMar1
• src/hg/utils/automation/doBlastzChainNet.pl
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    better line wrap in the README files, redmine 8887 note 94
• src/hg/utils/automation/makeDownloads.pl
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    better line wrap in the README files, redmine 8887 note 94
• src/hg/utils/automation/makeGenomeDb.pl
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    redmine issue 8707 HTML now reads HTTP
• src/product/README.mysql.setup
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    add note about LOCK TABLES for MySQL 5.5, redmine 9553
• src/product/ex.MySQLUserPerms.sh
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    add note about LOCK TABLES for MySQL 5.5, redmine 9553