Hey Guys,

It's great to receive so many responses! Thank you all for the
information...
and let me check out each of the masterpiece. :-)

Best,
Rui


On Wed, Sep 11, 2013 at 1:56 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> Wow - that makes at least five Deseq2 wrappers for Galaxy
> available or in progress :(
>
> Bjoern's wrapper on the (test) tool shed,
> http://testtoolshed.g2.bx.psu.edu/view/bgruening/deseq2
>
> Ross' combined wrapper for edgeR, DESeq2 and voom in one tool:
> http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models
>
> Joachim's wrapper on the Tool Shed
> http://toolshed.bits.vib.be/view/joachim/deseq2
>
> Vipin's which is soon to be released to the (Test?) Tool Shed,
> https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2
>
> And Rui's is working on one too.
>
> This does seem like duplicated effort & a source of confusion
> for end users and Galaxy administrators (a problem not unique
> to deseq2, but affecting many Galaxy wrappers).
>
> I appreciate there will be different needs, and one wrapper
> may not suit all, but I would prefer if the default behaviour
> for Galaxy tool wrapper authors was to collaborate on one
> good wrapper rather than writing competing ones.
>
> When I started work on a new wrapper I tried to announce
> this on the mailing list to find out if anyone else was already
> tackling the same tool - and that seemed to work quite well.
> Of course, the volume of emails on galaxy-dev has grown
> quite a lot over the last few years so that may not be as
> effective, but the archives should be searchable.
>
> Perhaps we need to improve communication in some way?
> One option would be to encourage greater use of the Test
> Tool Shed for works in progress to give them visibility?
> You could even have the Tool Shed itself require a search
> step before creating a new repository to avoid accidental
> duplication of effort? Or maybe a wiki page of wrappers
> in progress?
>
> (And maybe we should split this into a new thread)
>
> Regards,
>
> Peter
>
>
> On Wed, Sep 11, 2013 at 8:59 AM, Joachim Jacob | VIB |
> <joachim.ja...@vib.be> wrote:
> > Hi Rui,
> >
> > I should provide a 'sample metadata table', a tabular file with one
> column
> > the names of your samples, the other column the associated metadata (e.g.
> > type).
> >
> > This is how I've done it in my DESeq2 wrapper. :-) Feel free to check the
> > interface at http://toolshed.bits.vib.be/view/joachim/deseq2
> >
> >
> > Cheers,
> > Joachim
> >
> > Joachim Jacob
> > Contact details: http://www.bits.vib.be/index.php/about/80-team
> >
> >
> >
> > On 09/11/2013 01:15 AM, ruiwang.sz wrote:
> >>
> >> Hi All,
> >>
> >> we are making a wrapper for deseq2, and there is a step where
> >> control/experimental conditions
> >> need to be determined. For example, it would be a column like the
> >> following in the input file
> >>
> >> Type
> >> CTC
> >> CTC
> >> LM
> >> LM
> >> PT
> >> PT
> >>
> >> and we want the select list to contain
> >>
> >> CTC
> >> LM
> >> PT
> >>
> >> In other words, we want to filter out the 'Type' and have only distinct
> >> ones in the select list. We could
> >> make it in two steps, generate a intermediate file for this but it would
> >> be nice that we could directly
> >> retrieve the distinct types to make the list. I took a look at the tool
> >> config wiki, but didn't see anything
> >> (maybe because it was a quick scan). Does anyone have any tip on this?
> >> we'll really appreciate.
> >>
> >> Thanks,
> >> Rui
> >>
> >>
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