Excellent.  Thanks, Jeremy!

-b

On Fri, Jul 20, 2012 at 8:37 AM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> Brian,
>
> For the
> initial trinity de novo assembly, I took Jeremy's initial workflow and
> tweaked it to work with the latest release - and submitted it to the
> galaxy tool shed.
>
>
> Excellent. I'll remove my old Trinity wrapper from our code base and point
> people to your wrapper.
>
> There are some complexities here, such as not knowing ahead of time
> how many different samples are to be processed - so this needs to be
> determined dynamically, which impacts the overall complexity of the
> total workflow.  Is this possible in Galaxy, and if so, are there
> examples I can work from?
>
>
> Take a look at the repeat element; it enables a user to specify a number of
> inputs to a tool.
>
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crepeat.3E_tag_set
>
> Tool wrapper that use the repeat element include the GATK's depth of
> coverage and Cuffdiff.
>
> Best,
> J.



-- 
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
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