If I'm not mistaking, Composite Datatypes allow for only one directory, whereas we need to keep a constant directory structure with 2 or more sub-directories containing our input files.

We have no way to change these tools behavior (obviously not Galaxy-friendly ;-) ) and therefore need to maintain this structure in the job working directory.


Pierre Pericard
IE CDD - Projet Peptisan

Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX

Le 29/01/2013 17:47, Peter Cock a écrit :
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

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?



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