File Changes for hiram

v252_preview to v252_preview2 (2011-05-17 to 2011-05-31) v252

• src/hg/cartDump/cartDump.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/hgSession/hgSession.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/hgTables/galaxy.c
  • lines changed 1, context: html, text, full: html, text
    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/hgTables/great.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    WormBase link for ce10
  • lines changed 5, context: html, text, full: html, text
    provide WormBase link for cb4
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    no need to strip chr from cb4 chrom names for WormBase
• src/hg/hgc/wikiTrack.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/htdocs/images/phylo/anoCar2_7way.png
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    phylo image for anoCar2 7-way
• src/hg/lib/wikiLink.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/hg/makeDb/doc/anoCar2.txt
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    multiz run complete for 7-way
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    adding annotation rows to 7-way maf file
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    done with gene annotations on the 7-way maf
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    phylo tree estimate and phastCons done
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    phyloP done for 7-way
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    construct download files for 7-way
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    5000 and loose for gasAcu1 summary
• src/hg/makeDb/doc/caeJap4.txt
  • lines changed 231, context: html, text, full: html, text
    initial sequence is ready for genbank run
• src/hg/makeDb/doc/caePb3.txt
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    ready for genbank run as soon as kluster node rsync is done
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    done with genbank run
• src/hg/makeDb/doc/caeRem4.txt
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    initial makeGenomeDb.pl run
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    done with masking
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    running genbank alignments
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    done with genbank run
• src/hg/makeDb/doc/caeSp111.txt
  • lines changed 299, context: html, text, full: html, text
    ready for window masker cleaning
• src/hg/makeDb/doc/caeSp71.txt
  • lines changed 302, context: html, text, full: html, text
    running RM and TRF
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    running RM and TRF
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    ready for window masker cleaning
• src/hg/makeDb/doc/caeSp91.txt
  • lines changed 300, context: html, text, full: html, text
    ready for window masker cleaning
• src/hg/makeDb/doc/cb3.txt
  • lines changed 17, context: html, text, full: html, text
    liftover cb3 to cb4 and genbank done for ce10
• src/hg/makeDb/doc/cb4.txt
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    ready for genbank run
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    initial contents
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    done with genbank run
• src/hg/makeDb/doc/ce10.txt
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    initial genome build
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    ready for kluster activity
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    running genbank and set default position
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    set this as defaultDb in gateway page
  • lines changed 13, context: html, text, full: html, text
    liftover cb3 to cb4 and genbank done for ce10
• src/hg/makeDb/doc/ce4.txt
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    liftOver to ce10 done
• src/hg/makeDb/doc/ce6.txt
  • lines changed 18, context: html, text, full: html, text
    liftOver to ce10 done
• src/hg/makeDb/doc/ce9.txt
  • lines changed 18, context: html, text, full: html, text
    liftOver to ce10 done
• src/hg/makeDb/doc/ornAna1.txt
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    small correction to an old command
• src/hg/makeDb/genbank/etc/align.dbs
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    Added ce10 - C. elegans WS220
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    Added cb4 - C. briggsae WS220
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    Added caeRem4 C. remanei WS220
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    adding caePb3 C. brenneri WS220
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    adding ensGene for upstream table on anoCar2
  • lines changed 17, context: html, text, full: html, text
    Added ce10 C. elegans WS220
  • lines changed 22, context: html, text, full: html, text
    adding cb4 C. briggsae WS225
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    need a lift file for cb4
  • lines changed 19, context: html, text, full: html, text
    Added caeRem4 C. remanei WS220
  • lines changed 19, context: html, text, full: html, text
    Added caePb3 C. brenneri WS220
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added ce10 - C. elegans WS220
  • lines changed 1, context: html, text, full: html, text
    Added cb4 - C. briggsae WS220
  • lines changed 1, context: html, text, full: html, text
    Added caeRem4 C. remanei WS220
  • lines changed 1, context: html, text, full: html, text
    adding caePb3 C. brenneri WS220
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    override matrix for rheMac2
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 395, context: html, text, full: html, text
    description page ready to go for 7-way
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 5, context: html, text, full: html, text
    add notes about future names of several chrLG chroms
• src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
  • lines changed 104, context: html, text, full: html, text
    adding 7-way conservation definitions
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding ce10 to the browser
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    adding cb4 to the build
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    adding caeRem4 to the build
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    adding caeJap4 to the build
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    adding caeSp71 to the build
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    adding caeSp91 and caeSp111
• src/hg/makeDb/trackDb/worm/caeJap4/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 71, context: html, text, full: html, text
    adding caeJap4 to the build
• src/hg/makeDb/trackDb/worm/caeJap4/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 62, context: html, text, full: html, text
    adding caeJap4 to the build
• src/hg/makeDb/trackDb/worm/caeJap4/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 28, context: html, text, full: html, text
    adding caeJap4 to the build
• src/hg/makeDb/trackDb/worm/caeJap4/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caePb3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caePb3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caePb3/gold.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caePb3/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeRem4/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
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    Updated descriptions to match this release
• src/hg/makeDb/trackDb/worm/caeRem4/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 56, context: html, text, full: html, text
    Updated descriptions to match this release
• src/hg/makeDb/trackDb/worm/caeRem4/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
  • lines changed 40, context: html, text, full: html, text
    Updated descriptions to match this release
• src/hg/makeDb/trackDb/worm/caeRem4/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp111/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp111/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp111/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp111/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp71/description.html
  • lines changed 129, context: html, text, full: html, text
    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp71/gap.html
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    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp71/gold.html
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    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp71/trackDb.ra
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    initial source from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp91/description.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp91/gap.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp91/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeSp91/trackDb.ra
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/cb4/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/cb4/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/cb4/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/cb4/trackDb.ra
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    initial files from makeGenomeDb.pl
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    default vis for gold and gap
• src/hg/makeDb/trackDb/worm/ce10/description.html
  • lines changed 129, context: html, text, full: html, text
    initial contents from makeGenomeDb
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    update doc to represent actual assembly
• src/hg/makeDb/trackDb/worm/ce10/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial contents from makeGenomeDb
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    description.html
• src/hg/makeDb/trackDb/worm/ce10/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial contents from makeGenomeDb
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    description.html
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial contents from makeGenomeDb
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    description.html
• src/inc/cheapcgi.h
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    changing uses of cgiServerName to better cgiServerNamePort
• src/lib/cheapcgi.c
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    changing uses of cgiServerName to better cgiServerNamePort
• src/product/ex.hg.conf
  • lines changed 11, context: html, text, full: html, text
    add notes about how the wiki cookie names are constructed