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.

<datatype extension="dummy_zip" type="galaxy.datatypes.data:Data" mimetype="application/zip" display_in_upload="true" subclass="true" />

However, since our tools can be runned as a workflow and that most of them need this input directory we need to unzip it with R in the job working directory for each tool (about 5 times for the entire workflow).

Furthermore, this solution doesn't seem very "clean" if we want to share our tools via the ToolShed.

Is there a smart way to handle this kind of input directory that can be achieved with Galaxy default datatypes and/or that doesn't require to unzip a file each time we use a tool ?

Any update on a behavior change about zip files (http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005631.html) ?

Thanks in advance for any input,

Pierre

--
Pierre Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
http://abims.sb-roscoff.fr/

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