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

Ross Lazarus ross.lazarus at channing.harvard.edu
Sun Aug 3 04:11:57 CEST 2008

Hi, Mark - if you need any help finessing Galaxy, please don't hesitate 
to ask me directly as I'd be very happy to help. If you keep notes on 
your progress that we can repurpose as developer documentation for 
BioC/R developers, please send it along and I'll make sure it gets added 
to the Galaxy wiki.

Thanks for the pointers - I haven't looked at any of those - all the 
non-interactive R batch commands I've ever created have used the R 
commandArgs vector which allows direct access to the CL parameters 
without any muss or fuss - the counting is a bit strange because of the 
way R has to be called to run in batch mode, but something like this at 
the end of a script can be made to work easily in my experience - at 
least on linux:

(...R functions and package loading stuff to setup the main function 
htmlPlots in this case deleted for brevity...)

ca = commandArgs()
nargs = length(ca)
if (nargs < 7) # must be 7 if called correctly so whinge and bailout
print("Usage: R --vanilla --slave --args froot abspath imageurl < 
print("Please supply a file root for the input .xls file and an absolute 
path for output and an url for images\n")

froot = ca[5]
workdir = ca[6]
imageurl = ca[7]
# if testing, see what we got
# cat(paste('workdir=',workdir,'froot=',froot,'imageurl=',imageurl))

Mark Cowley wrote:
> 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.
> URLs:
> http://dirk.eddelbuettel.com/code/littler.html
> relative merits of littler vs RScript: 
> http://dirk.eddelbuettel.com/code/littler/README
> 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!

Ross Lazarus MBBS MPH, Director of Bioinformatics
Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA.

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