[BioC] Is anyone developing an extensible Galaxy-like interface for Bioconductor?

Mark Cowley m.cowley at garvan.org.au
Sun Aug 3 03:42:53 CEST 2008

Hi list,
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;
>>> charset=US-ASCII
>>> 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?
> <disclosure>
> I'm a galaxy developer so my views are probably biased
> </disclosure>
> 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  
> http://g2.trac.bx.psu.edu/wiki/AddToolTutorial
> 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  
> November.
> 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  
> 404614043
> The information transmitted in this electronic communica... 
> {{dropped:16}}
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