Commits for braney

v300_preview2 to v300_base (2014-05-12 to 2014-05-19) v300

• update hgGene to use new SCOP URL format
  • src/hg/hgGene/domains.c - lines changed 1, context: html, text, full: html, text
• a few tweaks to the hg38 knownGene page
  • src/hg/makeDb/trackDb/human/hg38/knownGene.html - lines changed 3, context: html, text, full: html, text
• remove CCDS from text
  • src/hg/makeDb/trackDb/human/hg38/knownGene.html - lines changed 6, context: html, text, full: html, text
• some tweaks to hg38/knownGene.html and making hg38 the default assemblyfor blastTabs on mm10, rn4, dm3, ce6, sacCer3
  
  • src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/knownGene.html - lines changed 8, context: html, text, full: html, text
• skunk project
  • src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adding the ability to search hubs for content.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 96, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hubPublic.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hubPublic.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/hubPublicCheck/hubPublicCheck.c - lines changed 14, context: html, text, full: html, text
• add knownToHprd
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh - lines changed 5, context: html, text, full: html, text
• clean up hgNearData to remove all the various human assembly dirsbecause they had (nearly) the same data. This results in hg38 support
  for Wanker, Vidal, and P2P.
  
  • src/hg/near/hgNear/hgNearData/Human/acc.html - lines changed 2, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/columnDb.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg17/columnDb.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg17/orderDb.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg18/acc.html - lines changed 2, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg18/columnDb.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg18/orderDb.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg19/acc.html - lines changed 2, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg19/columnDb.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/hg19/orderDb.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/near/hgNear/hgNearData/Human/orderDb.ra - lines changed 19, context: html, text, full: html, text
• load Vidal, Wanker, and P2P gene sorter tables
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh - lines changed 8, context: html, text, full: html, text
• fix pennantIcon code to reflect the documentation.
  • src/hg/lib/hui.c - lines changed 15, context: html, text, full: html, text
• fix bug with crashing hgc pages #13262
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text