Commits for hiram

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

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