Commits for steve

v258_base to v259_preview (2011-10-10 to 2011-10-25) v259

• Added link to 1000 Genomes Project. Changed journal link to point to open source article at oxfordjournals.org. Made some other minor formatting changes.
  • src/hg/makeDb/trackDb/human/hiSeqDepth.html - lines changed 7, context: html, text, full: html, text
• Moved period from inside hyperlink to outside hyperlink
  • src/hg/makeDb/trackDb/human/hiSeqDepth.html - lines changed 1, context: html, text, full: html, text
• Added bosTau6
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs - lines changed 1, context: html, text, full: html, text
• Added Katrina's track hub suggestions to the Setup Step 7 section
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 19, context: html, text, full: html, text
• Added tip about adding multiple tracks to a single custom track submission
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 3, context: html, text, full: html, text
• Change 'chicken' to 'turkey'
  • src/hg/makeDb/trackDb/turkey/melGal1/description.html - lines changed 1, context: html, text, full: html, text
• Changed example URL for including URL of track hub in browser URL
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 7, context: html, text, full: html, text
• Commented out link to VCF page as it is not yet on the RR
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 4, context: html, text, full: html, text
• Added include statement to other makefile
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile - lines changed 1, context: html, text, full: html, text
• Added chainMinScore override for monDom5 because getChainLines.csh script reported different value from what was on chain/net description page. Removed matrix override from monDom5 for same reason.
  • src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
• Added chainMinScore and chainLinearGap override for bosTau6 because getChainLines.csh script reported different value from what was on chain/net description page. Removed matrix override from bosTau6 for same reason.
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Added a link to the Track Lines section of the page. Removed 'bigWig' from the sentence to indicate that not only bigWig files can be specified.
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 3, context: html, text, full: html, text
• Changed file to designate old lizard/cow chain/nets by their database name
  • src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Changed file to designate old lizard/zebrafish chain/nets by their database name
  • src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• Changed file to designate old lizard chain/nets by their database name
  • src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra - lines changed 1, context: html, text, full: html, text
• Added override to old lizard/opossum/zebrafish chain/nets to use database name as track name
  • src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra - lines changed 5, context: html, text, full: html, text
• Removed override from monDom5 to allow organism name as track name
  • src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Removed override from bosTau6 chain/net so organism name would be the track name. Added override to bosTau4 chain/net so database name would be the track name. Added priority to bosTau4 so it would be grouped with bosTau6.
  • src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Added/removes overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text
• Added/removes overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra - lines changed 11, context: html, text, full: html, text
• Added/removed overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name
  • src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Added/removes overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra - lines changed 18, context: html, text, full: html, text
• Added/removes overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra - lines changed 11, context: html, text, full: html, text
• Removed unneeded overrides
  • src/hg/makeDb/trackDb/rat/rn4/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Added/removed overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• Added/removed overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/human/trackDb.chainNet.ra - lines changed 6, context: html, text, full: html, text
• Added/removed overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/lizard/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• Added/removed overrides so that old assemblies would use database name as the track name and new assemblies would use the organism name as the track name. Adjusted priorities so old/new assembly tracks appeared together in the track list.
  • src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• Added override section for xenTro2 so chain/net track would use database name as track name
  • src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra - lines changed 2, context: html, text, full: html, text
• Journal link was being redirected to a new URL. Changed the link to point directly to the new URL.
  • src/hg/makeDb/trackDb/ensGene.html - lines changed 1, context: html, text, full: html, text
• Added override section for melGal1
  • src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra - lines changed 4, context: html, text, full: html, text
• Added override section for melGal1
  • src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra - lines changed 3, context: html, text, full: html, text
• Added multiple override sections so that values on the description page would match script output
  • src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra - lines changed 20, context: html, text, full: html, text
• Fixed broken link to the SGD. Made other formatting changes.
  • src/hg/makeDb/trackDb/sacCer/sacCer2/sgdGene.html - lines changed 4, context: html, text, full: html, text
• Fixed broken link to the SGD. Made other formatting changes.
  • src/hg/makeDb/trackDb/sacCer/sacCer2/sgdOther.html - lines changed 3, context: html, text, full: html, text
• Corrected wording
  • src/hg/makeDb/trackDb/sacCer/sacCer2/sgdOther.html - lines changed 2, context: html, text, full: html, text
• Fixed broken link to the SGD
  • src/hg/makeDb/trackDb/sacCer/sacCer3/sgdGene.html - lines changed 3, context: html, text, full: html, text