Commits for steve

v277_base to v278_preview (2012-12-18 to 2013-01-08) v278

• Updated links; fixed so links would open in a new window
  • src/hg/makeDb/trackDb/human/hg19/cosmic.html - lines changed 11, context: html, text, full: html, text
• Updated links to the now-defunct baboon.math.berkeley.edu server; updated links to Mercator
  • src/hg/makeDb/trackDb/drosophila/geneMapper.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMavidAlign.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMavidCons.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/slamMouse.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/slamNonCodingMouse.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/slamNonCodingRat.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/slamRat.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/slamHuman.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/slamNonCodingHuman.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/slamHuman.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/slamNonCodingHuman.html - lines changed 6, context: html, text, full: html, text
• Fixed broken links
  • src/hg/makeDb/trackDb/firstEF.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/vistaEnhancers.html - lines changed 1, context: html, text, full: html, text
• Removed extraneous 'boliviensis' from saiBol1 Latin name
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/indexNews.html - lines changed 1, context: html, text, full: html, text
• Resolving merge conflict
• Removed extraneous 'boliviensis' from saiBol1
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/indexNews.html - lines changed 1, context: html, text, full: html, text
• Updated photo links
  • src/hg/makeDb/trackDb/apis/apiMel1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau6/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau7/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer5/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer6/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/description.html - lines changed 1, context: html, text, full: html, text
• Updated photo links
  • src/hg/makeDb/trackDb/chicken/galGal2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal4/description.html - lines changed 1, context: html, text, full: html, text
• Updated link
  • src/hg/makeDb/trackDb/pig/susScr2/description.html - lines changed 1, context: html, text, full: html, text
• Updated link
  • src/hg/makeDb/trackDb/affyAllExonProbes.html - lines changed 1, context: html, text, full: html, text
• Updated photo link (redmine #9153)
  • src/hg/makeDb/trackDb/lamprey/petMar1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/description.html - lines changed 1, context: html, text, full: html, text
• Changed 'cpgIsland%' to 'cpgIslandExt' - cpgIslandExt was not being recognized in the tables ignored list
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• Made minor corrections (redmine #9153)
  • src/hg/makeDb/trackDb/lamprey/petMar2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/gap.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/gold.html - lines changed 4, context: html, text, full: html, text
• Updated links in References section; made other minor corrections (redmine #9153)
  • src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html - lines changed 64, context: html, text, full: html, text
• Added petMar2 to hgwbeta.dbs; fixed ordering in hgwdev.dbs (redmine #9153)
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 2, context: html, text, full: html, text
• Fixed entries in the 'Gene tracks used for codon translation' table (redmine #9153)
  • src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html - lines changed 2, context: html, text, full: html, text
• Added priority section for petMar2 to various trackDb.chainNet.ra files; adjusted release tags for petMar1/2 chainNet.ra files in the main trackDb.chainNet.ra file (redmine #9153)
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text
• Adjusted release tags for petMar1/2 (redmine #9153)
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text
• Added petMar2 (redmine #9153)
  • src/hg/makeDb/genbank/etc/rr.dbs - lines changed 1, context: html, text, full: html, text