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.gruening@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.jacob@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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