But this only works if you have a single dataset (such as a BAM file) for each 
workflow to run on.
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...

Thon
Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839
thondeb...@me.com
LinkedIn Profile




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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