Hi John, Alex, All,

Elaborating on the motivation behind my question of running tools within
tool. First, running a tool in parallel at large-scale. For example, if I
need to find a pattern from 1000 files via Galaxy Select tool from Text and
Filter tool-group, I am limited by providing one file at a time to the tool
which will take a long time to finish. Please correct me if there is a more
sophisticated way to approach this problem. Second, related concern is
running a tool in parallel on one or more HPC resources.

We want to write a generic wrapper Galaxy tool, powered by Swift parallel
framework such that it can run any arbitrary Galaxy tool in parallel on HPC
resources. Currently, we have developed this capability but for external
executables which is not a most secure way of using Galaxy as I understand
from previous conversation.

Having such a wrapper tool in a standard way is desirable so that it
preserves the tool contract and binding within Galaxy environment. That is
maintaining the history and metadata conventions of Galaxy.

Thanks,
Ketan


On Wed, Feb 5, 2014 at 3:53 PM, John Chilton <chil...@msi.umn.edu> wrote:

> Galaxy has an API that is capable of running tools - certainly this is
> one path forward on something like this. I am not sure it is the best
> path forward though. Probably the best way to enhance Galaxy's
> execution capabilities is to extend the Galaxy core framework itself -
> this has its own downsides though.
>
> If you can offer more details about how you would like to enhance
> Galaxy - what it cannot do that you would like it to do - I or others
> may be able to provide more specific ideas. Otherwise, sorry I have
> not been or more help.
>
> -John
>
>
>
> On Tue, Feb 4, 2014 at 2:51 PM, Ketan Maheshwari <ke...@mcs.anl.gov>
> wrote:
> > Hi,
> >
> > This is a question I posted to galaxy user mailing list a while back and
> was
> > redirected to dev for possible answers:
> > Is it possible in Galaxy to design a tool whose sole purpose is to run
> other
> > tools. This is motivated by our desire to enhance execution capabilities
> of
> > existing tools via a generic tool which acts as a wrapper.
> >
> > Thanks,
> > Ketan
> >
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-- 
Ketan
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