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 > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > >
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