Yes I am agreeing on all statements.
Let me finish my package and will add in one of the toolshed by today
evening. I also willing to test other wrappers to improve the additional
parameter settings.

Tool wrappers Work In Progress from my side:
DEXSeq
edgeR
Scripture
STAR aligner
SAFT multi mapper resolution

This will be adding soon to the toolshed.

Thanks to all, Vipin

On Wed, Sep 11, 2013 at 6:08 AM, Bjoern Gruening
<bjoern.gruen...@gmail.com>wrote:

> Am Mittwoch, den 11.09.2013, 10:21 +0100 schrieb Peter Cock:
> > On Wed, Sep 11, 2013 at 10:12 AM, Joachim Jacob | VIB |
> > <joachim.ja...@vib.be> wrote:
> > > It is not necessarily bad. If we all test each others tools
> (dependencies,
> > > interface, output,...) we might get to the best of all worlds :-)  (I
> have
> > > planned to test Björns wrapper)
> > >
> > > One of the points of differentiation is also how 'integrated' a tool
> needs
> > > to be: e.g. Ross' tool for diff expression (combining a complete
> pipelin),
> > > and my tool just on DE with DESeq2. I like to keep things granular on
> the
> > > level of the tools.
> >
> > That is a good reason for different wrappers, one for the tool itself,
> > and one for a larger pipeline using the same tool. And both can
> > declare a binary package dependency via the Tool Shed using
> > the binary dependency package Bjoern is working on, which I
> > assume will be released on the Test & Main Tool Shed under
> > the shared IUC account once ready:
> >
> > http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_deseq2_1_0_17
>
>
> Yes that is right, at the moment I have patches for the toolshed in
> preparation for a unified and easy installation of R dependencies, once
> that is done it will be under the IUC account.
>
> I don't see the need for 5 different wrappers. Ross approach deserves an
> own wrapper I think. I thought a lot about if we should use it, since it
> can compare 3 different approaches for DE, but it comes with some
> complexity. We spend some time in trying to get the UI correct and
> investigated some possibilities. Currently we have a few guys testing it
> and giving comments to our UI idea. If the ownershop is a problem, we
> probably can move the wrappers to a different account. But please lets
> merge the code base and start communicating about the UI.
>
> Thanks,
> Bjoern
>
> > Regards,
> >
> > Peter
> >
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>
>
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