If you have pairs of files (such as paired end FASTQ files, not an uncommon workflow nowadays :) ) you need to resort to using the API, since there is no support for paired end sequencing in GALAXY in this batch processing from the UI (yet?). You can run the Workflow one at a time, but you have to choose the FASTQ pairs your self.

I have written a fairly generic execution engine that I can share, that uses a config file to describe the files you need from the library in simple key:value pairs and that can execute the paired-end sequencing on hundreds of FASTQ files...It's a little hacky and requires your FASTQ files to have some consistent naming for the forward and reverse reads (_R1.fastq & _R2.fastq) but other than that it seems to do the job...

There is however a nasty bug in the API, in that it removes the files from your history if you use them in the API (I will post something on that later) but it seems to work fine for data in the libraries...

On Jul 4, 2012, at 12:19 AM, Bernd Jagla wrote:

Dannon Baker <dannonbaker@...> writes:

Hi Dave,

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.

-Dannon

Dannon,

what if I don't have this icon??? How can I enable this? Where is this
documented?

Thanks,

Bernd

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