Commits for hiram

v248_base to v249_preview (2011-03-08 to 2011-03-15) v249

• only monDom5 and mm9 chain net left to go
  • src/hg/makeDb/doc/panTro3.txt - lines changed 83, context: html, text, full: html, text
• this clean target wasn't descending into USE_DIRS
  • src/utils/makefile - lines changed 6, context: html, text, full: html, text
• adding chain net overrides for all panTro3 related chain net combinations
  • src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra - lines changed 16, context: html, text, full: html, text
• eliminate use of HOME in MYLIBDIR
  • src/hg/oneShot/dupedInTable/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/kgName/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/musAliAt/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/protDat/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/testCart/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/testTableExists/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/weedKnownBlastTab/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/weedTab/makefile - lines changed 1, context: html, text, full: html, text
• properly clean the executable
  • src/utils/bigBedSummary/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• eliminate use of HOME in MYLIBDIR
  • src/hg/autoXml/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/bedOverlap/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpHiQualDiffs/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/chimpStuff/chimpSuperQuals/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/geneBounds/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/geneOverlap/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/logCrawl/hgAccessCrawl/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/doOmimAv/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pslToFa/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/balancedTree/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/findContigsWithClones/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/foo2/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/formatFastaSeq/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/mafFindZero/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/newStitch4/makefile - lines changed 1, context: html, text, full: html, text
  • src/oneShot/test/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/dataSim/makefile - lines changed 1, context: html, text, full: html, text
  • src/reformat/makeOrf2gene/makefile - lines changed 2, context: html, text, full: html, text
• update to include trix and metaDb files and properly rsync js and style directories
  • src/product/scripts/fetchMinimalGbdb.sh - lines changed 4, context: html, text, full: html, text
  • src/product/scripts/fetchMinimalGoldenPath.sh - lines changed 2, context: html, text, full: html, text
  • src/product/scripts/updateHtml.sh - lines changed 6, context: html, text, full: html, text