Commits for hiram

v288_preview2 to v288_base (2013-08-13 to 2013-08-19) v288

• reenable trix building in San Diego refs #8132
  • src/hg/makeDb/trackDb/makefile - lines changed 3, context: html, text, full: html, text
• proper clean target for TEST_DIRS refs #9149
  • src/hg/makefile - lines changed 5, context: html, text, full: html, text
• do not need the host hgwdevSD refs #8875
  • src/hg/utils/cpAndLinkToResourceFiles.pl - lines changed 1, context: html, text, full: html, text
• forget trix annulment clause, refs #8132
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• MySQL 5.6 uses the ENGINE variable in place of TYPE refs #8875
  • src/hg/checkTableCoords/tests/input/fakeChromInfo.sql - lines changed 1, context: html, text, full: html, text
• fixup sorting of outputs and expected to avoid MySQL sorting differences refs #9149
  • src/hg/hgGetAnn/tests/makefile - lines changed 6, context: html, text, full: html, text
• missing the build of the sqlCheck binary for the testing refs #8875
  • src/hg/lib/tests/makefile - lines changed 1, context: html, text, full: html, text
• eliminate duplcated named file that has outlived usefulness refs #8875
  • src/hg/lib/encode/unused/shortFrags.as - lines changed 31, context: html, text, full: html, text
• update cosmic to v66 refs #10158
  • src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
• install move should remove target first refs #9149
  • src/inc/cgi_build_rules.mk - lines changed 4, context: html, text, full: html, text
• inform messages about where log file exists for script results and echo messages to stederr refs #9104
  • src/product/scripts/fetchMinimalGbdb.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/kentSrcUpdate.sh - lines changed 9, context: html, text, full: html, text
  • src/product/scripts/minimal.db.list.txt - lines changed 64, context: html, text, full: html, text
  • src/product/scripts/updateHtml.sh - lines changed 9, context: html, text, full: html, text
• adding track INSDC name refs #11348
  • src/hg/lib/ucscToINSDC.as - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/ucscToINSDC.sql - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 9, context: html, text, full: html, text
• adding track INSDC name refs #11348
  • src/hg/makeDb/doc/hg19.txt - lines changed 48, context: html, text, full: html, text
• finishing merge
• adding search rule and html doc for ucscToINSDC track refs #11348
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ucscToINSDC.html - lines changed 16, context: html, text, full: html, text
• fixup comments about path name refs #9409
  • src/hg/makeDb/doc/oviAri3.txt - lines changed 1, context: html, text, full: html, text
• fixup comments about path name refs #10833
  • src/hg/makeDb/doc/vicPac2.txt - lines changed 1, context: html, text, full: html, text
• adding Ostrich - Struthio camelus refs #10272
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 3, context: html, text, full: html, text
• adding ucscToINSDC track refs #11348
  • src/hg/makeDb/doc/gorGor3.txt - lines changed 81, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/doc/nomLeu3.txt - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/doc/panPan1.txt - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/panTro4.txt - lines changed 43, context: html, text, full: html, text
• v288 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 6, context: html, text, full: html, text
• New version number v288
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text