File Changes for hiram

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 2, context: html, text, full: html, text
    add WGS link to NCBI
• src/hg/makeDb/doc/fr3.txt
  • lines changed 366, context: html, text, full: html, text
    done with genbank and starting lastz runs with other fish
  • lines changed 96, context: html, text, full: html, text
    first set of lastz runs done, experiment underway with gasAcu1
  • lines changed 45, context: html, text, full: html, text
    done with gasAcu1 lastz experiments and all fish lastz runs
• src/hg/makeDb/doc/gasAcu1.txt
  • lines changed 59, context: html, text, full: html, text
    add WGS link information, and document the WindowMasker run
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 22, context: html, text, full: html, text
    first pass of 11-way multiz has been loaded
• src/hg/makeDb/doc/oreNil1.txt
  • lines changed 234, context: html, text, full: html, text
    done with masking, prepare for kluster runs
  • lines changed 1, context: html, text, full: html, text
    make a comment actually a comment
  • lines changed 19, context: html, text, full: html, text
    add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 2, context: html, text, full: html, text
    add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
• src/hg/makeDb/doc/tetNig2.txt
  • lines changed 3, context: html, text, full: html, text
    add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 2, context: html, text, full: html, text
    add blat server for tilapia and default position, minor notes in oryLat2, tetNig2 and xenTro3
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added fr3.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    no lift file for fr3
  • lines changed 1, context: html, text, full: html, text
    no per-chrom tables on fr3
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added fr3.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding oreNil1 to the build
• src/hg/makeDb/trackDb/oreNil/oreNil1/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/oreNil/oreNil1/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/oreNil/oreNil1/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/oreNil/oreNil1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    do not allow the reference species to exist on the sGroup_vertebrate line
• src/hg/utils/phyloTrees/57way.dissect.txt
  • lines changed 791, context: html, text, full: html, text
    the result of: /cluster/bin/phast/tree_doctor --dissect 57way.nh > 57way.dissect.txt
• src/hg/utils/phyloTrees/57way.nh
  • lines changed 26, context: html, text, full: html, text
    adding hetGla1,sarHar1,croPor1,aliMis1,latCha1,oreNil1
• src/inc/common.mk
  • lines changed 7, context: html, text, full: html, text
    full -Werror only on hgwdev, too much trouble for mirror sites
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    add note about creating namedSessionDb table
• src/product/scripts/README
  • lines changed 6, context: html, text, full: html, text
    add note about second rsync server option
• src/product/scripts/browserEnvironment.txt
  • lines changed 3, context: html, text, full: html, text
    indicate secondary rsync server available