Commits for hiram

v252_base to v253_preview (2011-06-07 to 2011-06-14) v253

• adding caeJap4 to the build
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• lastz runs done for almost all to ce10
  • src/hg/makeDb/doc/caeJap4.txt - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeRem4.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp111.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp71.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp91.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/cb4.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/ce10.txt - lines changed 301, context: html, text, full: html, text
• finished with all lastz operations to ce10
  • src/hg/makeDb/doc/caeAng1.txt - lines changed 315, context: html, text, full: html, text
  • src/hg/makeDb/doc/caePb3.txt - lines changed 142, context: html, text, full: html, text
  • src/hg/makeDb/doc/ce10.txt - lines changed 124, context: html, text, full: html, text
• ce10 9way multiz tree
  • src/hg/htdocs/images/phylo/ce10.9way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• nematode tree enlarged
  • src/hg/utils/phyloTrees/nematode.14way.nh - lines changed 1, context: html, text, full: html, text
• adjust some branch lengths given lastz chain net coverage
  • src/hg/utils/phyloTrees/nematode.14way.nh - lines changed 1, context: html, text, full: html, text
• incorrect file name
  • src/hg/htdocs/images/phylo/ce10.9way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct file name
  • src/hg/htdocs/images/phylo/ce10_9way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• 9-way multiz initial done and ensGene v62 loaded
  • src/hg/makeDb/doc/ce10.txt - lines changed 195, context: html, text, full: html, text
• maf gaps annotated and phastCons and phyloP runs done
  • src/hg/makeDb/doc/ce10.txt - lines changed 563, context: html, text, full: html, text
• downloads have been constructed
  • src/hg/makeDb/doc/ce10.txt - lines changed 81, context: html, text, full: html, text
• text from ce9 cons10way and edited for this 9-way alignment
  • src/hg/makeDb/trackDb/worm/ce10/cons9way.html - lines changed 403, context: html, text, full: html, text
• adding 9-way multiple alignment definition
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 110, context: html, text, full: html, text
• perhaps better order of organisms in phylo distance maybe
  • src/hg/makeDb/trackDb/worm/ce10/trackDb.ra - lines changed 1, context: html, text, full: html, text
• reference to hgdownload-test instead of hgdownload
  • src/hg/makeDb/trackDb/worm/ce10/cons9way.html - lines changed 5, context: html, text, full: html, text
• makeDownloads.pl has been run and all README files in download directories have been edited
  • src/hg/makeDb/doc/caeAng1.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeJap4.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/caePb3.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeRem4.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp111.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp71.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeSp91.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/cb4.txt - lines changed 13, context: html, text, full: html, text
• adding caePb3 to the build
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text