Can you attach your XML wrapper and R script or part of them ? I will take a look on them.
Gildas ----------------------------------------------------------------- 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 http://abims.sb-roscoff.fr ------------------------------------------------------------------ > Le 5 févr. 2016 à 17:30, rbrown1...@comcast.net a écrit : > > Good morning Gildas, > After moving my <command R .... outside of the <stdio /> block below -- > this fixed worked > FYI the Rscript in the same tool dir has issues with reading a dataset > from the directory. Seems like permissions but isn't. > Thank you > Bob Brown > ----- Original Message ----- > From: Gildas Le Corguillé <lecorgui...@sb-roscoff.fr> > To: rbrown1...@comcast.net > Cc: John Chilton <jmchil...@gmail.com>, galaxy-dev@lists.galaxyproject.org > Sent: Fri, 05 Feb 2016 08:27:07 -0000 (UTC) > Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see > Datafile in History smaller email size > Hi, > 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 : > <stdio> > <exit_code range="1:" level="fatal" /> > </stdio> > 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 > ----------------------------------------------------------------- > 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 > http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> > ------------------------------------------------------------------ > > > Le 4 févr. 2016 à 21:25, rbrown1...@comcast.net > <mailto:rbrown1...@comcast.net> a écrit : > > John, > 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 > GREEN? > thanks. > bob > ----- Original Message ----- > From: John Chilton <jmchil...@gmail.com <mailto:jmchil...@gmail.com>> > To: rbrown1...@comcast.net <mailto:rbrown1...@comcast.net>, > galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.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. > -John > On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchil...@gmail.com > <mailto: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: > > > > $__tool_directory__/Foo.R > > > > -John > > > > > > On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1...@comcast.net > > <mailto:rbrown1...@comcast.net>> wrote: > >> Good morning team, > >> I have an Rscript tool that is trying to read a file I uploaded into the > >> history beforehand. Galaxy is running with the same user and privileges as > >> the dataset directory. > >> <command>Rscript --slave --vanilla > >> --file=$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 > >> > >> > >> ___________________________________________________________ > >> 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: > >> https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > >> <http://galaxyproject.org/search/mailinglists/> > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/>
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