File Changes for hiram

v306_preview to v306_preview2 (2014-09-08 to 2014-09-15) v306

• src/hg/htdocs/images/Bundibugyo_ebolavirus.jpg
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    from wikimedia commons CDC Public Health Image Library 10816
• src/hg/htdocs/images/Ebola_virus.jpg
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    generic ebola virus photo refs #13996
• src/hg/htdocs/images/Marburg_virus.jpg
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    adding marVir1 refs #13996
• src/hg/htdocs/images/Reston_ebolavirus.jpg
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    adding resEbo1 refs #13995
• src/hg/htdocs/images/Sudan_ebolavirus.jpg
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    adding sudEbo1 refs #13994
• src/hg/htdocs/images/Tai_Forest_ebolavirus.jpg
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    adding taiEbo1 refs #13997
• src/hg/htdocs/images/Zaire_ebolavirus.jpg
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    adding zaiEbo1 refs #13996
• src/hg/htdocs/images/phylo/eboVir2_49way.png
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    adding initial eboVir2 49-way tree diagram refs #13996
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    better 49-way diagram eboVir2 refs #1396
• src/hg/makeDb/doc/dm6.txt
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    27 way multiz done refs #4049
• src/hg/makeDb/trackDb/ebola/bunEbo1/description.html
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    initial files from makeGenomeDb.pl refs #13993
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    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/bunEbo1/gap.html
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    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/bunEbo1/gold.html
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    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/bunEbo1/trackDb.ra
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    initial files from makeGenomeDb.pl refs #13993
• src/hg/makeDb/trackDb/ebola/eboVir1/description.html
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    ebola virus 46 strains refs #13996
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    indicate where the list of strains are from refs #13996
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    indicate where the list of strains are from refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/gap.html
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    ebola virus 46 strains refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/gold.html
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    ebola virus 46 strains refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir1/trackDb.ra
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    ebola virus 46 strains refs #13996
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    adding chainSelf refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/description.html
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    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
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    adding 49-way multiz track refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/gap.html
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    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/gold.html
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    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
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    adding 49-way multiz track refs #13996
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    correct reference to phylo tree image refs #13996
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    extra names on the known named strains refs #13996
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    do not need the eboVir2 mention on the sGroup_Virus refs #13996
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    visual clustering to order strains refs #13996
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    visual clustering to order strains refs #13996
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    eliminate stray blank line refs #13996
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    visual clustering to order strains refs #13996
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    visual clustering to order strains refs #13996
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    visual clustering to order strains refs #13996
• src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
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    now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
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    adding 47-strain (self) chain alignments refs #13996
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    default full viz adding 47-strain (self) chain alignments refs #13996
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    added genePredictions track from blatting proteins refs #13996
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    adding 47-strain (self) chain alignments refs #13996
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    setting default viz refs #13996
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    setting default viz refs #13996
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    adding 49-way multiz track refs #13996
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    viz on self chain to hide refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/description.html
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/gap.html
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/gold.html
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/marVir1/trackDb.ra
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/resEbo1/description.html
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    adding resEbo1 refs #13995
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    fixup assembly links refs #13994 #13995
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    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/gap.html
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    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/gold.html
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    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/resEbo1/trackDb.ra
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    adding resEbo1 refs #13995
• src/hg/makeDb/trackDb/ebola/sudEbo1/description.html
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    adding sudEbo1 refs #13994
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    fixup assembly links refs #13994 #13995
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    fixup photo reference with full name refs #13993 #13994 #13995
• src/hg/makeDb/trackDb/ebola/sudEbo1/gap.html
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/sudEbo1/gold.html
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/sudEbo1/trackDb.ra
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    adding sudEbo1 refs #13994
• src/hg/makeDb/trackDb/ebola/taiEbo1/description.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/gap.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/gold.html
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/taiEbo1/trackDb.ra
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    adding trackDb for taiEbo1 refs #13997
• src/hg/makeDb/trackDb/ebola/trackDb.chainNet.ra
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    adding chain tracks for 4 others to zaiEbo1 refs #13996
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    adding lastz marVir1 refs #13996
• src/hg/makeDb/trackDb/ebola/trackDb.ra
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    adding NCBI annotation track refs #13993 #13994 #13995 #13996 #13997
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    adding chain tracks for 4 others to zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/description.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gap.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/gold.html
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/ebola/zaiEbo1/trackDb.ra
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    adding trackDb for zaiEbo1 refs #13996
• src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/chainNetStray.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
• src/hg/makeDb/trackDb/human/hg38/description.html
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    fixup accession ID refs #11706
• src/hg/makeDb/trackDb/makefile
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    adding bunEbo1 to the build refs #13993
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    adding sudEbo and resEbo1 to the build refs 3994 #13995
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    adding taiEbo1 zaiEbo1 to the build refs #13996 #13997
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    adding ebola virus 46 strains refs #13996
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    adding eboVir2 refs #13996
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    adding marVir1 refs #13996
• src/hg/makeDb/trackDb/tagTypes.tab
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    adding 49-way multiz track refs #13996
• src/hg/utils/phyloTrees/eboVir2.49way.nh
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    eboVir2 Nway trees mostly from Baize et.al 2014-04-25 NEJM and visually added extras refs #13996
• src/hg/utils/phyloTrees/eboVir2.53way.nh
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    eboVir2 Nway trees mostly from Baize et.al 2014-04-25 NEJM and visually added extras refs #13996
• src/userApps/fetchKentSource.sh
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    adding hgLoadOutJoined to the fetch refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
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    v306 preview2 refs #13954