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
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,
Head of Genome Biology Computational Support (GBCS)
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
69117 Heidelberg, Germany
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