Clarification on urls setting, and new sections about useOneFile and Assembly Hubs

[Brian Lee]

If applicable to your hubs, please see some clarifications about the setting  urls <fieldName1>="<url1>" <fieldName2>="<url2>". This setting allows additional fields in a bigBed, besides the 4th "name" field, to build links out on the details page: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#urls

These fields can contain multiple values, separated by a comma "," where multiple links will then be created on each item. For instance, a field named "pmid"  with an entry "11932250,34718705" would create two links. If an entry of comma-separated values contains a "|" symbol, the part before the pipe symbol is used to replace the $$ wildcard and the part after it is used as the label, as opposed to the default label description in the .as file.  This can be handy for both providing a unique label for each link, and having multiple link outs for some items, while others may only have one or no link.

To help advertise that Track Hubs with only one genome can take advantage of the  useOneFile on in the hub.txt stanza, there is a new paragraph near the top of the document pointing to more details: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#useOneFile

Also, to help explain that many additional settings in the genomes.txt file exist specific to Assembly Hubs, such as groups, organism, defaultPos, twoBitPath, htmlPath a  new paragraph linking to more information on these settings has been added: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#assembly_hubs