[BioC] Bioconductor Digest, Vol 66, Issue 2 Message 7 (apologies; long and veering off topic)

Ross Lazarus ross.lazarus at channing.harvard.edu
Sun Aug 3 02:44:58 CEST 2008

>> 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?

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 

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 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

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