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:
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
and my tool just on DE with DESeq2. I like to keep things granular on
Am Mittwoch, den 11.09.2013, 10:21 +0100 schrieb Peter Cock: pipelin), 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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