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Question: Fetch Sequences for multiple datasets
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gravatar for Abdullah
4.5 years ago by
Abdullah • 0
Abdullah • 0 wrote:

I uploaded ~60 bed files to the public galaxy server and I want to 'Fetch Sequences' for the coordinates for all of them (each of them is independent file from others). Do I need to do click 'Fetch Sequences' for each of them. Is there any feature to apply this command to all/selected files?
galaxy • 1.1k views
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modified 4.5 years ago by Wolfgang Maier • 600 • written 4.5 years ago by Abdullah • 0
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gravatar for Wolfgang Maier
4.5 years ago by
Wolfgang Maier • 600
Germany
Wolfgang Maier • 600 wrote:

You can use a simplistic workflow for that:

- create a new workflow and edit it to contain a run of the fetch sequences tool as its only step

- connect an input dataset to it and save the workflow

When you run your workflow note the little file icons next to Input Dataset. This is where you enable multiple input datasets. If you do so, Galaxy runs one job per input dataset.

Cheers,

Wolfgang
ADD COMMENT • link written 4.5 years ago by Wolfgang Maier • 600
2

As of this coming June release - you will be able to dynamically select multiple inputs on all tool data parameters to get this behavior (one job per dataset) without needing to create the one step workflows. https://trello.com/c/14OxiyMv.

ADD REPLY • link written 4.5 years ago by jmchilton ♦ 1.1k

great to hear that, thanks!

ADD REPLY • link written 4.5 years ago by Wolfgang Maier • 600

Thanks very much @WlfgangMaier for the detailed explanation and thanks @jmchilton for the good news.

ADD REPLY • link written 4.5 years ago by Abdullah • 0
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