On Tue, Jan 29, 2013 at 4:41 PM, Pierre Pericard
<pierre.peric...@sb-roscoff.fr> wrote:
> Hi all,
>
> We've just added some new tools based on R scripts to our local Galaxy
> instance.
>
> Most of these tools need to work at the root of the directory containing the
> input files (up to hundreds of XML files) spread among two or more
> sub-directories. The directory structure need to be kept since the R tools
> recursively search for files and use the subdirectories names as classes.
>
> To solve this problem we added a "dummy" datatype to our instance so we can
> upload the input directory as a zip file without Galaxy decompressing it.

Have you looked at a composite datatype instead, where the files are
stored on disk decompressed?

http://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes

Peter
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