Question: Running R In Galaxy
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gravatar for Bree, Freddy de
7.2 years ago by
Bree, Freddy de80 wrote:
I've been trying to run R in Galaxy. 1. Running it as "R" is a hassle, because Galaxy cannot deal with source and input file and output file using "--args" and "<" (< in xml) and ">" (> in xml). 2. Running it through "perl" is also a hassle, because Galaxy needs to have an input file through the cmd line, whilst "R" needs: - input file (the location of it, not the content) - source file (.R file) - output file BUT you need to pipe -this- input for perl through to R VIA the system() call. Anybody any luck with this? (everything runs without Galaxy btw, but that is not the aim) Freddy
galaxy • 2.7k views
ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Bree, Freddy de80
0
gravatar for Sean Davis
7.2 years ago by
Sean Davis220
Sean Davis220 wrote:
Have you tried littler as a scripting engine? http://dirk.eddelbuettel.com/code/littler.html That is only one potential solution. Sean
ADD COMMENTlink written 7.2 years ago by Sean Davis220
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gravatar for James Taylor
7.2 years ago by
James Taylor470
United States
James Taylor470 wrote:
We use a small shell script called r_wrapper.sh which is included in the distribution.
ADD COMMENTlink written 7.2 years ago by James Taylor470
There is also now RScript http://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html since R distro before that there was littelr too http://code.google.com/p/littler/ Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA To: Bree, Freddy de Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] running R in Galaxy We use a small shell script called r_wrapper.sh which is included in the distribution. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
ADD REPLYlink written 7.2 years ago by Cook, Malcolm30
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gravatar for Bree, Freddy de
7.2 years ago by
Bree, Freddy de80 wrote:
Dear all, In addition tot he previous. I can feed the source file (Rfile) and the data file to the system() call for R, but how do I capture the output back in perl? Freddy
ADD COMMENTlink written 7.2 years ago by Bree, Freddy de80
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gravatar for Bree, Freddy de
7.2 years ago by
Bree, Freddy de80 wrote:
Thanks again! This solves it I think. I re-directed this to galaxy-user, because it is clear that some of you do not know this either. ;) ________________________________________ To: Bree, Freddy de Subject: Re: [galaxy-user] running R in Galaxy Yes, tools/stats/r_wrapper.sh
ADD COMMENTlink written 7.2 years ago by Bree, Freddy de80
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gravatar for Bree, Freddy de
7.2 years ago by
Bree, Freddy de80 wrote:
Following the discussion on this topic, the solution: You can run R 'straight' in galaxy without a wrapper: <command>R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Rscript --args $infile $outfile</command> The input is never a big problem in galaxy, but how to capture the output was not so clear to me. So, Make sure your output file can be seen by galaxy (which was basically my problem): <inputs> <param name="infile" type="data" format="tabular"/> </inputs> <outputs> <data name="outfile" type="data" format="tabular"/> </outputs> And in R making sure, the output file has a name as well: write.table(data, sep="\t", file=out.file, row.names=F) Thanks for all the help!!
ADD COMMENTlink written 7.2 years ago by Bree, Freddy de80
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