But this only works if you have a single dataset (such as a BAM file) for each workflow to
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 de Boer, Ph.D.
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
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.
what if I don't have this icon??? How can I enable this? Where is this
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