Yes, we have considered using data libraries, but for this particular use case we would
prefer an approach like this. Our users are notoriously bad at data management and we
would like to limit the amount of data that gets loaded in Galaxy. The networked share
does not store all data permanently, so we need something to query what is available so
the users can load that into their history.
Ideally the datasets also shouldn’t be copied into Galaxy, but symlinked, if possible.
Thanks for the tip on ‘dynamic_options’. Hadn’t noticed it before.
Op 19 jan. 2016, om 13:40 heeft Hans-Rudolf Hotz <hrh(a)fmi.ch>
het volgende geschreven:
Have you considered "Data Libraries"?
A cron job can query your LIMS and use the API to create "Data Libraries". Then
the user can select which datasets she/he wants to import.
And back to your original question: Yes, it is possible to create interactive tools.
Check out the 'dynamic_options' examples on
On 01/19/2016 12:18 PM, Matthias De Smet wrote:
> Hi All,
> I would like to create a tool to import data from a sequencer on a networked share to
a users history.
> The ideal setup would be that a query can be submitted to a database which contains
all metadata from the sequencer + the path of the sequencer output. The tool should then
show the available datasets found in the database and provide checkboxes to select which
data should be imported.
> My question is: how do you guys propose I get started on this? Do I use the API? Is
it even possible to get a tool to return some output without submitting it as a job, e.g.
using it interactively?
> Thanks for the help!
> PS: I know the basics of tool development, but I haven’t got much experience, so all
comments are welcome!
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