Hi Eric,

I have no current resources or active users for microarray development
so I can't contribute much and although the rgenetics code works fine
with galaxy central the rexpression code is way out of date - which is
why the metadata handling is so broken. There are ongoing problems in
galaxy central with composite objects - downloads, pages and other
things have been broken for a long time - so fixes would definitely be
welcome.

As far as the design goes, the challenge is representing complex R
objects like expressionsets in Galaxy. The composite representation is
a complex solution with the advantage that the pheno data is available
for the user to (eg) select variables for limma - which would
otherwise not be very convenient in a Galaxy tool form which can't go
into R to read the phenoData slot.

I'd be very happy to see the project continue so will provide whatever
help I can...

On Fri, Nov 18, 2011 at 10:50 AM, Paniagua, Eric <epani...@cshl.edu> wrote:
> Hi Ross,
>
> That's excellent, thanks for jumping in!
>
> I've been charged with constructing a Galaxy tool kit for basic microarray 
> data analysis for my group's Galaxy instance, and I looked at your Rgenetics 
> / Rexpression (more the latter of course) as a starting point.  I was 
> wondering how the compatibility of your tools and datatypes with plain old 
> galaxy-dist is going these days.  I've wound up rewrapping or rewriting some 
> of your tools because they didn't seem to be working out of the box.  Minor 
> path problems weren't hard to fix.  More major problems had to do with 
> incomplete / broken ways that the Galaxy core handles composite datasets.
>
> So I'm wondering if you've kept up active development over the last few 
> months and found good workarounds.  (I don't want to hijack this thread, so 
> perhaps a private reply or a new thread makes sense.)
>
> Best,
> Eric
>
> ________________________________
> From: Ross [ross.laza...@gmail.com]
> Sent: Thursday, November 17, 2011 8:47 PM
> To: Paniagua, Eric
> Cc: Timothy Wu; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Name your own tool's output?
>
> Hi Timothy, if by "customize the name of the output" you mean "display a 
> string of my choice as the new history item display name" then yes.
>
> Eric - thanks for reminding me to fix that old code!
> :)
>
> Post execution hooks are not needed - there's a much cleaner way - eg given a 
> form field "usersuppliedlabel", something like
> <outputs>
>    <data format="foo" name="output"  label="$usersuppliedlabel">
>  ...
> The label becomes the history item display name if that helps?
>
> On Thu, Nov 17, 2011 at 8:26 PM, Paniagua, Eric 
> <epani...@cshl.edu<mailto:epani...@cshl.edu>> wrote:
> Hi Timothy,
>
> Check out tools/rgenetics/rgLDIndep.xml and the associated 
> tools/rgenetics/rgLDIndep_code.py for an example of how to change the name of 
> your output data.
>
> Best,
> Eric
>
> ________________________________
> From: 
> galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>
>  
> [galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>]
>  on behalf of Timothy Wu [2hug...@gmail.com<mailto:2hug...@gmail.com>]
> Sent: Wednesday, October 12, 2011 4:51 AM
> To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
> Subject: [galaxy-dev] Name your own tool's output?
>
> Hi,
>
> I thought I had already asked this question a while ago, but I can't find it 
> so I guess I haven't.
>
> When porting my own tool, is there anyway to customize the name of the output?
>
> Timothy
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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