Running R In Galaxy

Question: Running R In Galaxy

8.2 years ago by

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 • 3.3k views

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modified 8.1 years ago • written 8.2 years ago by Bree, Freddy de • 90

8.2 years ago by

Sean Davis • 220

Sean Davis • 220 wrote:

Have you tried littler as a scripting engine? http://dirk.eddelbuettel.com/code/littler.html That is only one potential solution. Sean

ADD COMMENT • link written 8.2 years ago by Sean Davis • 220

8.2 years ago by

James Taylor ♦ 470

United States

James Taylor ♦ 470 wrote:

We use a small shell script called r_wrapper.sh which is included in the distribution.

ADD COMMENT • link written 8.2 years ago by James Taylor ♦ 470

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 REPLY • link written 8.2 years ago by Cook, Malcolm • 30

8.2 years ago by

Bree, Freddy de • 90

Bree, Freddy de • 90 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 COMMENT • link written 8.2 years ago by Bree, Freddy de • 90

8.2 years ago by

Bree, Freddy de • 90

Bree, Freddy de • 90 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 COMMENT • link written 8.2 years ago by Bree, Freddy de • 90

8.1 years ago by

Bree, Freddy de • 90

Bree, Freddy de • 90 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!!

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