Supporting file sets for running a tool with multiple input files
Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>
Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card ( https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be adding a new datatype, say, ZippedInputFiles in your toolshed repository that gets included and used by users, though I haven't actually tried that. That said, I'd probably wait, this feature is high on our list of things to do next. -Dannon On Mon, Nov 4, 2013 at 5:44 AM, Lukasse, Pieter <pieter.lukasse@wur.nl>wrote:
Hi,
Is there any news regarding support for the following scenario in Galaxy:
- User has N files which he would like to process with a Galaxy tool using the same parameters
- User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool
- Tool produces an output .zip file with the N result files
I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base?
Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)?
Thanks and regards,
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
+31-317480891; skype: pieter.lukasse.wur
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Hi Dannon, Thanks for your reply. I've found a workaround by using the method Binary.register_sniffable_binary_format() . I discovered this workaround in a previous thread by John Chilton. Attached the complete solution, just for the record. Regards, Pieter. From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: maandag 4 november 2013 13:42 To: Lukasse, Pieter Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Supporting file sets for running a tool with multiple input files Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card (https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be adding a new datatype, say, ZippedInputFiles in your toolshed repository that gets included and used by users, though I haven't actually tried that. That said, I'd probably wait, this feature is high on our list of things to do next. -Dannon On Mon, Nov 4, 2013 at 5:44 AM, Lukasse, Pieter <pieter.lukasse@wur.nl<mailto:pieter.lukasse@wur.nl>> wrote: Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891<tel:%2B31-317480891>; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/> ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Dannon Baker -
Lukasse, Pieter