The directory can be obtained using $galaxyData.extra_files_path (be
sure to check it exists before zipping it up).
I would discourage re-using Galaxy components directly from inside of
a tool or tool wrapper - but if you want to reference that code it is
actually inside of the datatypes module -
Hope this helps.
On Tue, Mar 11, 2014 at 5:35 AM, Charles Girardot
> Hi all,
> We have a local tool which role is to transfer (ie copy) a dataset file to a
> directory on our NFS. This is extremely convenient as it can be included
> within workflows and therefore save the time of clicking download button (we
> also have configurable renaming/compression as part of it). It is heavily
> used by our users.
> The problem is with datasets that have associated files like FASTQC as these
> extra files are simple not ignored...
> We'd like to improve our 'NFS_transfer' tool so it can deal with this in a
> similar fashion as the download button.
> Foreseen solution :
> * Check if a directory named 'dataset_<id>_files' exists within the dataset
> * if so, 'cp -r' it into a tmp dir, cp the dataset itself into same tmp dir
> (with renaming on the fly)
> * zip/tar.gz the tmp dir
> * copy it to final NFS location
> Question is : is this the right way to do it ? As a non python specialist,
> it is a little tricky to find the right way to it (I can t locate the piece
> of code that does this in galaxy ie behind the download button). In
> particular, can I get the list of extra files using the '$galaxyFile' object
> given in the tool by :
> <param type="data" name="galaxyFile" label="File to transfer"/>
> i.e. in the same way we get the dataset name or file extension
> ($galaxyFile.dataset.name and $galaxyFile.ext) ?
> Any advise on how best to implement this, in a portable way, very appreciated.
> Thanks for your time,
> Charles Girardot
> Head of Genome Biology Computational Support (GBCS)
> European Molecular Biology Laboratory
> Tel: +49 6221 387 -8585
> Fax: +49-(0)6221-387-8166
> Email: charles.girar...@embl.de
> Room V205
> Meyerhofstraße 1,
> 69117 Heidelberg, Germany
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