Hi Aaron, If you are designing a new datatype for a (set of) tool(s) and this datatype requires a bunch of files to be in a directory and these files are generally only useful when they are bundled together as a single unit (i.e. you wouldn't normally want any one of the files to exist as a separate history item), then you may want to look at composite datasets: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes That works well for user-supplied data. If you just want to provide reference data for users, a look into the tool_data_tables would be a good start. Thanks for using Galaxy, Dan On Apr 4, 2012, at 1:48 PM, Aaron Gallagher wrote:
On Apr 4, 2012, at 8:11 AM, Langhorst, Brad wrote:
I think I would approach the directory problem with a wrapper script that takes arguments for each of the components needed by the tool. The script could lay out the various files as expected in the working directory and call the script. I think that's cleaner than expecting users to build a tar archive with the proper structure.
Sorry if I wasn't more clear: the tools take _the entire directory_ (which we call reference packages, to be less ambiguous in the rest of this e-mail) as the input, not parts of it passed separately. Building these reference packages is not a problem. They're a fundamental part of a lot of analyses we do, and as such, we have tools to build them easily. For the Galaxy instance I'm trying to set up, though, most of the reference packages that users need will be provided as shared data.
~Aaron
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