Because R always return blabla in the standard error output (stderr), by
default Galaxy thinks that there is a problem. You need this following lines in
your wrapper xml :
<exit_code range="1:" level="fatal" />
With that, Galaxy will use the code error (echo $?) instead of the stderr to
detect an error.
Another thing, you can use
<command interpreter="Rscript">Foo.R $inputFile1 ..... </command>
If your script is in the same folder as your xml
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)
Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
> Le 4 févr. 2016 à 21:25, rbrown1...@comcast.net a écrit :
> Thanks for the great info. I got the R to work not the Rscript.
> However, my data files return RED even though there is data in them
> I am still getting R warning but no errors
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C"
> 2: Setting LC_COLLATE failed, using "C"
> 3: Setting LC_TIME failed, using "C"
> 4: Setting LC_MESSAGES failed, using "C"
> 5: Setting LC_MONETARY failed, using "C"
> 6: Setting LC_PAPER failed, using "C"
> 7: Setting LC_MEASUREMENT failed, using "C"
> Is there a flag I can set to igrore these warning and have Galaxy return
> ----- Original Message -----
> From: John Chilton <jmchil...@gmail.com>
> To: rbrown1...@comcast.net, firstname.lastname@example.org
> Sent: Thu, 04 Feb 2016 20:11:53 -0000 (UTC)
> Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see
> Datafile in History smaller email size
> Forgot to cc the mailing list.
> On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchil...@gmail.com> wrote:
> > Are you sure about the --file when calling Rscript?
> > Here is the usage for my local version which does not expect an
> > argument named --file:
> > Usage: /path/to/Rscript [--options] [-e expr] file [args]
> > --options accepted are
> > --help Print usage and exit
> > --version Print version and exit
> > --verbose Print information on progress
> > --default-packages=list
> > Where 'list' is a comma-separated set
> > of package names, or 'NULL'
> > or options to R, in addition to --slave --no-restore, such as
> > --save Do save workspace at the end of the session
> > --no-environ Don't read the site and user environment files
> > --no-site-file Don't read the site-wide Rprofile
> > --no-init-file Don't read the user R profile
> > --restore Do restore previously saved objects at startup
> > --vanilla Combine --no-save, --no-restore, --no-site-file
> > --no-init-file and --no-environ
> > 'file' may contain spaces but not shell metacharacters
> > Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__
> > if the tool XML file is located next to the RScript, like this:
> > $__tool_directory__/Foo.R
> > -John
> > On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1...@comcast.net> wrote:
> >> Good morning team,
> >> I have an Rscript tool that is trying to read a file I uploaded into the
> >> history beforehand. Galaxy is running with the same user and privileges as
> >> the dataset directory.
> >> <command>Rscript --slave --vanilla
> >> --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 ..... </command>
> >> Why would this be?
> >> Error in file(file, "rt") : cannot open the connection
> >> Calls: performDataOrdering -> read.table -> file
> >> In addition: Warning message:
> >> In file(file, "rt") :
> >> cannot open file
> >> '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such
> >> file or directory
> >> Execution halted
> >> When I try to run as R versus Rscript - I get a syntax error about
> >> unexpected '(' on function call that works fine in R window.
> >> Thanks
> >> Bob
> >> ___________________________________________________________
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: