The directory can be obtained using $galaxyData.extra_files_path (be
sure to check it exists before zipping it up).
I would discourage re-using Galaxy components directly from inside of
a tool or tool wrapper - but if you want to reference that code it is
actually inside of the datatypes module -
https://bitbucket.org/galaxy/galaxy-central/src/3fb927653301a0c06a0bf94f2b6bd71b3595ec0d/lib/galaxy/datatypes/data.py?at=default#cl-228
Hope this helps.
-John
On Tue, Mar 11, 2014 at 5:35 AM, Charles Girardot
charles.girar...@embl.de wrote:
Hi all,
We have a local tool which role is to transfer (ie copy) a dataset file to a
directory on our NFS. This is extremely convenient as it can be included
within workflows and therefore save the time of clicking download button (we
also have configurable renaming/compression as part of it). It is heavily
used by our users.
The problem is with datasets that have associated files like FASTQC as these
extra files are simple not ignored...
We'd like to improve our 'NFS_transfer' tool so it can deal with this in a
similar fashion as the download button.
Foreseen solution :
* Check if a directory named 'dataset_id_files' exists within the dataset
store
* if so, 'cp -r' it into a tmp dir, cp the dataset itself into same tmp dir
(with renaming on the fly)
* zip/tar.gz the tmp dir
* copy it to final NFS location
Question is : is this the right way to do it ? As a non python specialist,
it is a little tricky to find the right way to it (I can t locate the piece
of code that does this in galaxy ie behind the download button). In
particular, can I get the list of extra files using the '$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
=
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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