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
On Tue, Sep 21, 2010 at 5:30 AM, Bree, Freddy de <freddy.debree@wur.nl>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?
Have you tried littler as a scripting engine? http://dirk.eddelbuettel.com/code/littler.html That is only one potential solution. Sean
On Sep 21, 2010, at 5:30 AM, Bree, Freddy de wrote:
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).
We use a small shell script called r_wrapper.sh which is included in the distribution.
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 -----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of James Taylor Sent: Tuesday, September 21, 2010 6:06 AM To: Bree, Freddy de Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] running R in Galaxy On Sep 21, 2010, at 5:30 AM, Bree, Freddy de wrote:
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).
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
participants (4)
-
Bree, Freddy de -
Cook, Malcolm -
James Taylor -
Sean Davis