Commits for hiram

v306_preview2 to v306_base (2014-09-15 to 2014-09-22) v306

• adding 102-way multiz alignment refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.102way.ra - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adding 102-way strain name cross reference refs #13996
  • src/hg/makeDb/doc/eboVir2/ucscName.strainName.sed - lines changed 104, context: html, text, full: html, text
• extracted descriptions from genbank records refs #13996
  • src/hg/makeDb/doc/eboVir2/153.strain.descriptions.txt - lines changed 153, context: html, text, full: html, text
• adding UCSC naming scheme refs #13996
  • src/hg/makeDb/doc/eboVir2/153.strain.descriptions.txt - lines changed 153, context: html, text, full: html, text
• adding Angie names from yesterday refs #13996
  • src/hg/makeDb/doc/eboVir2/ucscName.strainName.sed - lines changed 48, context: html, text, full: html, text
• eliminate duplicate entries, add duplicate sequences, add Marburg all names accounted for refs #13996
  • src/hg/makeDb/doc/eboVir2/ucscName.strainName.sed - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir2/virus.strain.descriptions.txt - lines changed 155, context: html, text, full: html, text
• better short label refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• better short label refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra - lines changed 3, context: html, text, full: html, text
• adding five more from the Baize paper refs #13996
  • src/hg/makeDb/doc/eboVir2/158.strain.descriptions.txt - lines changed 158, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir2/ucscName.strainName.sed - lines changed 104, context: html, text, full: html, text
• corrected 1966 date to 1996 refs #13996
  • src/hg/makeDb/doc/eboVir2/158.strain.descriptions.txt - lines changed 1, context: html, text, full: html, text
• fetching sequence information refs #14011
  • src/hg/makeDb/doc/eboVir3/fetchSequence.txt - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/gbkDefinition.pl - lines changed 55, context: html, text, full: html, text
• setting mafDot on refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.102way.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra - lines changed 1, context: html, text, full: html, text
• document regular track construction refs #13996
  • src/hg/makeDb/doc/eboVir2/ordinaryTracks.txt - lines changed 82, context: html, text, full: html, text
• document regular track construction refs #13996
  • src/hg/makeDb/doc/eboVir2/ordinaryTracks.txt - lines changed 15, context: html, text, full: html, text
• West Africa instead of Sierra Leone refs #13396
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.102way.ra - lines changed 5, context: html, text, full: html, text
• experiment with name.name maf file spec refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
• correct first two nodes that multiz did not understand refs #13996
  • src/hg/utils/phyloTrees/eboVir2.49way.nh - lines changed 44, context: html, text, full: html, text
• comment out self chain tracks and rename those tables refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 14, context: html, text, full: html, text
• cpgIsland override refs #13996
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 18, context: html, text, full: html, text
• same photo from eboVir2 for eboVir3 under a more generic name refs #14011
  • src/hg/htdocs/images/Filoviridae_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 #14011
  • src/hg/makeDb/trackDb/ebola/eboVir3/description.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding eboVir3 refs #14011
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• correct nucleotide reference refs #14011
  • src/hg/makeDb/trackDb/ebola/eboVir3/description.html - lines changed 2, context: html, text, full: html, text
• setting default viz refs #14011
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra - lines changed 4, context: html, text, full: html, text
• initial track building refs #14011
  • src/hg/makeDb/doc/eboVir3/lastz160way.txt - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt - lines changed 154, context: html, text, full: html, text
• running 160-way on eboVir3 refs 4011
  • src/hg/makeDb/doc/eboVir3/fetchSequence.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/lastz160way.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/multiz160way.txt - lines changed 124, context: html, text, full: html, text
• first view of 160-way refs #14011
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra - lines changed 2, context: html, text, full: html, text
• first view of 160-way refs #14011
  • src/hg/makeDb/doc/eboVir3/multiz160way.txt - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt - lines changed 7, context: html, text, full: html, text
• now with strain names, missing one for some odd reason refs 4011
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra - lines changed 38, context: html, text, full: html, text
• 16-way now showing strain names refs #14011
  • src/hg/makeDb/doc/eboVir3/multiz160way.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/eboVir3/ucscName.strainName.sed - lines changed 160, context: html, text, full: html, text
• species group names are getting longer than 24 characters refs #13411
  • src/hg/hgTracks/wigMafTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 5, context: html, text, full: html, text
• ordered by visual similarity and grouped refs #14011
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.160way.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.strainName160way.ra - lines changed 10, context: html, text, full: html, text
• ordered by visual similarity and grouped refs #14011
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 10, context: html, text, full: html, text
• sloth was out of order refs #11681
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 3, context: html, text, full: html, text
• allow hg.conf override of 5000 pixel wide limit refs #10411
  • src/hg/lib/trackLayout.c - lines changed 8, context: html, text, full: html, text
• allow hg.conf override of 5000 pixel wide limit refs #10411
  • src/hg/inc/trackLayout.h - lines changed 1, context: html, text, full: html, text
• allow hg.conf override of 5000 pixel wide limit refs #10411
  • src/product/ex.hg.conf - lines changed 4, context: html, text, full: html, text
• catch up with the stray outcast KJ660347v2 which had the incorrect db name in its pairwise refs #14011
  • src/hg/makeDb/doc/eboVir3/multiz160way.txt - lines changed 21, context: html, text, full: html, text
• add blat servers refs #14011
  • src/hg/makeDb/doc/eboVir3/ordinaryTracks.txt - lines changed 2, context: html, text, full: html, text
• v306 final build refs #13832
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v306
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text