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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