Yes, galaxy's standard run-workflow dialog has a feature where you can select multiple datasets as input for a single "Input Dataset" step. To do this, click the icon referenced by the tooltip in the screenshot below to select multiple files. All parameters remain static between executions except for the single input dataset that gets modified for each run, and that only one input dataset can be set to multiple files in this fashion.

On Feb 6, 2012, at 4:18 PM, Dave Lin wrote:

Hi All,

I'm looking to batch process 40 large data sets with the same galaxy workflow.

This obviously can be done in a brute-force manual manner.

However, is there a better way to schedule/invoke these jobs in batch

1) from the UI with a plugin
2) command-line
3) web-service

Thanks in advance for any pointers.
Dave

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