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!
Matthias
Hi Matthias
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
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Regards, Hans-Rudolf
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!
Matthias ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans-Rudolf
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.
Matthias
Op 19 jan. 2016, om 13:40 heeft Hans-Rudolf Hotz hrh@fmi.ch het volgende geschreven:
Hi Matthias
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
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Regards, Hans-Rudolf
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!
Matthias ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
Hans-Rudolf Hotz -
Matthias De Smet