Commits for steve

v276_base to v277_preview (2012-11-20 to 2012-12-03) v277

• Updated mouse miRNA tracks to point to miRBase per Rachel (redmine #9598)
  • src/hg/makeDb/trackDb/miRNA.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm8/miRNA.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/miRNA.html - lines changed 7, context: html, text, full: html, text
• Added dasNov3, ochPri2, oreNil2, otoGar3 and panTro4
  • src/hg/makeDb/genbank/etc/rr.dbs - lines changed 5, context: html, text, full: html, text
• Modified script so it doesn't print output unless it actually finds broken links; will make the output much easier to interpret for assemblies with a large number of tables
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 12, context: html, text, full: html, text
• Also edited the section that checks the description page to only print output if it finds broken links
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 6, context: html, text, full: html, text
• Added an error counter and a summary line in the output so in the event of no errors, there wouldn't just be a blank output file
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 15, context: html, text, full: html, text
• Moved line to delete error file outside of if-statement - otherwise, the error file only gets deleted if there is an error; also added a line to ignore '403 from http://hgwbeta.cse.ucsc.edu/cgi-bin/' as a valid error
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 6, context: html, text, full: html, text
• Corrected references to old menu items in the blue top navigation bar (redmine #8900)
  • src/hg/htdocs/goldenPath/help/hgTracksHelp.html - lines changed 5, context: html, text, full: html, text
• Corrected the coordinates in the description of the example (redmine #9681)
  • src/hg/htdocs/goldenPath/help/bedgraph.html - lines changed 1, context: html, text, full: html, text
• Added a table counter and added the total table count to the summary section
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 7, context: html, text, full: html, text
• Added tables for the new 1000 Genomes tracks to the tablesIgnored section (redmine #1079,7964)
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• Made minor corrections, added software links, reformatted references (redmine #1079)
  • src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html - lines changed 49, context: html, text, full: html, text
• Changed number of individuals described in Methods section to 1,092 to match the journal title in the References section per Tom Blackwell (redmine #1079)
  • src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html - lines changed 1, context: html, text, full: html, text
• Fixed the track long label for 1000 Genomes Phase 1 Variant Calls - changed 'InDels' to 'Indels' (redmine #7964)
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Made minor formatting corrections; fixed References section (redmine #7964)
  • src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html - lines changed 30, context: html, text, full: html, text
• Shortened the long label for 1000 Genomes Accessibility Pilot Criteria subtrack so it was under 80 characters (redmine #1079)
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text