Commits for hiram

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

• 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 - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetStray.ra - lines changed 1002, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
• now packaging chainNet composites with a script and reign in the stray chain nets on hg19 refs #10272
  • src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra - lines changed 2, context: html, text, full: html, text
• 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 - lines changed 1, context: html, text, full: html, text
• adding hgLoadOutJoined to the fetch refs #9149
  • src/userApps/fetchKentSource.sh - lines changed 1, context: html, text, full: html, text
• fixup accession ID refs #11706
  • src/hg/makeDb/trackDb/human/hg38/description.html - lines changed 2, context: html, text, full: html, text
• 27 way multiz done refs #4049
  • src/hg/makeDb/doc/dm6.txt - lines changed 400, context: html, text, full: html, text
• from wikimedia commons CDC Public Health Image Library 10816
  • src/hg/htdocs/images/Bundibugyo_ebolavirus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• initial files from makeGenomeDb.pl refs #13993
  • src/hg/makeDb/trackDb/ebola/bunEbo1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/bunEbo1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/bunEbo1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/bunEbo1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding bunEbo1 to the build refs #13993
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding sudEbo1 refs #13994
  • src/hg/htdocs/images/Sudan_ebolavirus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding resEbo1 refs #13995
  • src/hg/htdocs/images/Reston_ebolavirus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding resEbo1 refs #13995
  • src/hg/makeDb/trackDb/ebola/resEbo1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding sudEbo1 refs #13994
  • src/hg/makeDb/trackDb/ebola/sudEbo1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding sudEbo and resEbo1 to the build refs 3994 #13995
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• fixup assembly links refs #13994 #13995
  • src/hg/makeDb/trackDb/ebola/resEbo1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/description.html - lines changed 3, context: html, text, full: html, text
• adding zaiEbo1 refs #13996
  • src/hg/htdocs/images/Zaire_ebolavirus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding taiEbo1 refs #13997
  • src/hg/htdocs/images/Tai_Forest_ebolavirus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding trackDb for zaiEbo1 refs #13996
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding trackDb for taiEbo1 refs #13997
  • src/hg/makeDb/trackDb/ebola/taiEbo1/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/taiEbo1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/taiEbo1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/taiEbo1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• fixup photo reference with full name refs #13993 #13994 #13995
  • src/hg/makeDb/trackDb/ebola/bunEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/description.html - lines changed 1, context: html, text, full: html, text
• adding taiEbo1 zaiEbo1 to the build refs #13996 #13997
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding NCBI annotation track refs #13993 #13994 #13995 #13996 #13997
  • src/hg/makeDb/trackDb/ebola/trackDb.ra - lines changed 6, context: html, text, full: html, text
• adding chain tracks for 4 others to zaiEbo1 refs #13996
  • src/hg/makeDb/trackDb/ebola/trackDb.chainNet.ra - lines changed 235, context: html, text, full: html, text
• adding chain tracks for 4 others to zaiEbo1 refs #13996
  • src/hg/makeDb/trackDb/ebola/trackDb.ra - lines changed 2, context: html, text, full: html, text
• generic ebola virus photo refs #13996
  • src/hg/htdocs/images/Ebola_virus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• ebola virus 46 strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding ebola virus 46 strains refs #13996
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• indicate where the list of strains are from refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir1/description.html - lines changed 2, context: html, text, full: html, text
• indicate where the list of strains are from refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir1/description.html - lines changed 1, context: html, text, full: html, text
• adding chainSelf refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir1/trackDb.ra - lines changed 14, context: html, text, full: html, text
• now with zaiEbo1 sequence included and NC names for the five NCBI sequences refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding eboVir2 refs #13996
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding 47-strain (self) chain alignments refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 14, context: html, text, full: html, text
• default full viz adding 47-strain (self) chain alignments refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• added genePredictions track from blatting proteins refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 9, context: html, text, full: html, text
• adding 47-strain (self) chain alignments refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• setting default viz refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 2, context: html, text, full: html, text
• setting default viz refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adding marVir1 refs #13996
  • src/hg/htdocs/images/Marburg_virus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding marVir1 refs #13996
  • src/hg/makeDb/trackDb/ebola/marVir1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/marVir1/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/marVir1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/marVir1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding marVir1 refs #13996
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• adding lastz marVir1 refs #13996
  • src/hg/makeDb/trackDb/ebola/trackDb.chainNet.ra - lines changed 59, context: html, text, full: html, text
• adding 49-way multiz track refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
• adding initial eboVir2 49-way tree diagram refs #13996
  • src/hg/htdocs/images/phylo/eboVir2_49way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct reference to phylo tree image refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• viz on self chain to hide refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• extra names on the known named strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 4, context: html, text, full: html, text
• do not need the eboVir2 mention on the sGroup_Virus refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• visual clustering to order strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• visual clustering to order strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• better 49-way diagram eboVir2 refs #1396
  • src/hg/htdocs/images/phylo/eboVir2_49way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• eliminate stray blank line refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• eboVir2 Nway trees mostly from Baize et.al 2014-04-25 NEJM and visually added extras refs #13996
  • src/hg/utils/phyloTrees/eboVir2.49way.nh - lines changed 49, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/eboVir2.53way.nh - lines changed 53, context: html, text, full: html, text
• visual clustering to order strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• visual clustering to order strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• visual clustering to order strains refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• v306 preview2 refs #13954
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text