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: rbrown1422@comcast.netCc: John Chilton
<jmchil...@gmail.com>, galaxy-dev@lists.galaxyproject.orgSent: 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/BioanalystePlateforme ABiMS (Analyses and
Bioinformatics for Marine Science)Station Biologique de Roscoff - UPMC/CNRS -
FR2424Place Georges Teissier 29680 Roscoff FRANCEtel: +33 2 98 29 23
81http://abims.sb-roscoff.fr------------------------------------------------------------------
Le 4 févr. 2016 à 21:25, 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>To:
rbrown1...@comcast.net, galaxy-dev@lists.galaxyproject.orgSent: 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> 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
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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:
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