[BioC] Is anyone developing an extensible Galaxy-like interface for Bioconductor?
m.cowley at garvan.org.au
Sun Aug 3 03:42:53 CEST 2008
We have been thinking about plugging in some of our generic routines
(like QC) into the Galaxy interface.
There are at least 3 useful ways of making R code more 'script-like',
including the built in RScript, 'littler', and the CRAN library getopt.
relative merits of littler vs RScript: http://dirk.eddelbuettel.com/
littler looks to be the most convenient of the three, but on OSX,
littler requires R to be compiled as a dylib, which I'm currently
doing, but is towards the bottom of my list of things to do, thus I
don't have any feedback on how useful it really is.
If anyone else has tried this, then some feedback would be great!
On 03/08/2008, at 10:44 AM, Ross Lazarus wrote:
>>> Message: 7 Date: Fri, 01 Aug 2008 15:52:22 -0400 From: "Deanne
>>> Taylor" <DTAYLOR at hsph.harvard.edu> Subject: [BioC] Is anyone
>>> developing an extensible Galaxy-like interface for Bioconductor? To:
>>> <bioconductor at stat.math.ethz.ch> Message-ID:
>>> <48933135.2DE5.00B2.0 at hsph.harvard.edu> Content-Type: text/plain;
>>> Dear all:
>>> Iis anyone aware of any projects creating an extensible platform
>>> that can act as an interface to Bioconductor that could be used to
>>> deliver Bioconductor methods to non-command-line-using users?
> I'm a galaxy developer so my views are probably biased
> Why not just use Galaxy to wrap the BioC packages? It will do what
> you need and probably a lot more.
> <potentially veering off topic>
> For those not yet aware, Galaxy (http://g2.trac.bx.psu.edu/) is an
> open-source framework for wrapping executables into a web
> application with workflows, persistent histories, transparent
> connections to popular annotation and data resources (BioMart/
> ucsc..) and a growing toolbox of applications - all of which
> completely insulate users from command lines. Galaxy started out
> with a focus on evolutionary biology and that's what's available at
> the main Galaxy site, but as a generic platform for a computational
> workspace, it is easy to reconfigure for your own requirements if
> you checkout the source and run it locally - which you need to do
> for IRB protected data of course.
> IMHO, Galaxy histories (persistent, shareable user workspaces
> containing complete records of all data, annotation,
> transformations and analyses) are one of the really important
> things it offers. Another strength is that it is completely
> agnostic to the actual plugin executable - anything that can run on
> the backend (potentially, a torque/SGE cluster) - java, R, C++ or
> heaven help us COBOL- as long as it takes parameters and is non-
> interactive - which means R scripts need to be written to take CL
> parameters rather than run in the interactive interpreter environment.
> You can checkout a working copy of Galaxy to your linux box or mac
> (see http://g2.trac.bx.psu.edu/wiki/HowToInstall). With your own
> copy, follow the tutorial on adding a new (ugh, perl) tool at
> Changing from perl to an R script wrapping a BioConductor package
> will require the following steps:
> 1) figure out exactly what package functions/analyses/
> transformation the tool will wrap and thus, what inputs, outputs
> and parameter settings you want the user to control;
> 2) write and test an R wrapper for the package which takes those
> parameters on the command line (must be non-interactive), reads
> it's inputs from files named on the command line, and writes it's
> outputs to files named on the command line;
> 3) provide the interface descriptor as XML which Galaxy uses to
> construct the right command line (including those inputs and
> outputs) for the plugin executable and the web form for the user to
> set the parameters which will be supplied to the executable (this
> is what you will probably need help with initially - the source
> distribution contains a lot of useful examples and the Galaxy dev
> mailing list is a friendly place to get help);
> 4) add your new XML descriptor file to the tool_config.xml file;
> 5) restart your local Galaxy.
> Some statistical genetics tools are visible at http://
> galaxy.esphealth.org based on R/plink/eigenstrat and so on and some
> of their uses are illustrated with some (now slightly dated)
> screencasts at http://esphealth.org/screencasts. For those
> attending, there are 3 educational sessions featuring Galaxy and
> the UCSC genome browser at the upcoming ASHG meeting in Philly in
> The Galaxy developer team is keen to help people wanting to develop
> new useful tools - in particular, we currently have no expression
> tools available. We're ready and willing to help anyone interested
> in using Galaxy to make BioConductor packages available to users in
> a web-accessible framework that really does encourage transparent
> and reproducible research.
> Contact me privately if you have questions please.
> </potentially veering off topic>
> Ross Lazarus MBBS MPH, Director of Bioinformatics
> Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA.
> Currently on vacation in Sydney: Tel +61 293657975 or Cell +61
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