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with galaxy central the rexpression code is way out of date - which is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
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.)
> From: Ross [ross.laza...@gmail.com]
> Sent: Thursday, November 17, 2011 8:47 PM
> To: Paniagua, Eric
> Cc: Timothy Wu; firstname.lastname@example.org
> 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
> <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.
> on behalf of Timothy Wu [2hug...@gmail.com<mailto:2hug...@gmail.com>]
> Sent: Wednesday, October 12, 2011 4:51 AM
> To: email@example.com<mailto:firstname.lastname@example.org>
> Subject: [galaxy-dev] Name your own tool's output?
> 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?
> 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;
Please keep all replies on the list by using "reply all"
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