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, rbrown1422@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 lecorguille@sb-roscoff.fr To: rbrown1422@comcast.net Cc: John Chilton jmchilton@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, rbrown1422@comcast.net mailto:rbrown1422@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 <jmchilton@gmail.com mailto:jmchilton@gmail.com> To: rbrown1422@comcast.net mailto:rbrown1422@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 <jmchilton@gmail.com mailto:jmchilton@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:
$__tool_directory__/Foo.R
-John
On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net mailto:rbrown1422@comcast.net> wrote:
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$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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