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> 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:
$__tool_directory__/Foo.R
-John
On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$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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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>To: rbrown1422@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 <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:>> $__tool_directory__/Foo.R>> -John>>> On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:>> Good morning team,>> I have an Rscript tool that is trying to read a file I uploaded into the>> history beforehand. Galaxy is running with the same user and privileges as>> the dataset directory.>> <command>Rscript --slave --vanilla>> --file=$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/>>>> To search Galaxy mailing lists use the unified search at:>> http://galaxyproject.org/search/mailinglists/
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 ------------------------------------------------------------------
Le 4 févr. 2016 à 21:25, 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> To: rbrown1422@comcast.net, 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> 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:
$__tool_directory__/Foo.R
-John
On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:
Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$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/
To search Galaxy mailing lists use the unified search at: 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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.netCc: John Chilton <jmchilton@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, 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>To: rbrown1422@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 <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:>> $__tool_directory__/Foo.R>> -John>>> On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1422@comcast.net> wrote:>> Good morning team,>> I have an Rscript tool that is trying to read a file I uploaded into the>> history beforehand. Galaxy is running with the same user and privileges as>> the dataset directory.>> <command>Rscript --slave --vanilla>> --file=$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/>>>> To search Galaxy mailing lists use the unified search at:>> 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 thisand other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ 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/>
participants (3)
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Gildas Le Corguillé -
John Chilton -
rbrown1422＠comcast.net