"Please keep all replies on the list by using "reply all""
well, what happens if you run
Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
<command> interpreter="bash">Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command>
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out now. thanks, Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad I don't you are using R to execute your R script.... How do you call your R script, ie how does the command tag looks in the tool definition file? Also, why do you have a "#!/bin/bash" at the beginning of your R script? Regards, Hans-Rudolf On 04/27/2014 09:50 PM, Bradley Belfiore wrote: I am new to galaxy and while trying to convert an R tool to a Galaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: syntax error near unexpected token `(' /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))' any help as to how to remedy this would be greatly appreciated. The first couple lines of my .R file are # #!/bin/bash args<-(commandArgs(TRUE)) Thanks, Brad _____________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
The initial error now seems to be taken care of and now am getting this message on attempting to run tool:
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 109, in __init__ commands = initial_command.rstrip("; ") AttributeError: 'NoneType' object has no attribute 'rstrip'
On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
"Please keep all replies on the list by using "reply all""
well, what happens if you run
Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments
Hans-Rudolf
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
<command> interpreter="bash">Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command>
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out now. thanks, Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad I don't you are using R to execute your R script.... How do you call your R script, ie how does the command tag looks in the tool definition file? Also, why do you have a "#!/bin/bash" at the beginning of your Rscript?
Regards, Hans-Rudolf On 04/27/2014 09:50 PM, Bradley Belfiore wrote: I am new to galaxy and while trying to convert an R tool to aGalaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:
syntax error near unexpected token `(' /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))' any help as to how to remedy this would be greatly appreciated.The first couple lines of my .R file are # #!/bin/bash args<-(commandArgs(TRUE))
Thanks, Brad _____________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ?
To me, it looks like you have a bug in your Rscript and/or your wrapper.
Hans-Rudolf
On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
The initial error now seems to be taken care of and now am getting this message on attempting to run tool:
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 109, in __init__ commands = initial_command.rstrip("; ") AttributeError: 'NoneType' object has no attribute 'rstrip'
On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
"Please keep all replies on the list by using "reply all"" well, what happens if you run Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata $pathwayid $species $output on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments Hans-Rudolf On 04/28/2014 03:32 PM, Bradley Belfiore wrote: Thank you for your quick response, my command tag is: <command> interpreter="bash">Rscript___wrapper.sh /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata $pathwayid $species $output </command> So I believe Im calling R via the Rscript_wrapper.sh? As far as the #!/bin/bash, not sure why I had that there, I took it out now. thanks, Bradley Belfiore On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: Hi Brad I don't you are using R to execute your R script.... How do you call your R script, ie how does the command tag looks in the tool definition file? Also, why do you have a "#!/bin/bash" at the beginning of your R script? Regards, Hans-Rudolf On 04/27/2014 09:50 PM, Bradley Belfiore wrote: I am new to galaxy and while trying to convert an R tool to a Galaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/____tools/pathview/pathview.R: line 1: syntax error near unexpected token `(' /Users/bmbelfio/galaxy-dist/____tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))' any help as to how to remedy this would be greatly appreciated. The first couple lines of my .R file are # #!/bin/bash args<-(commandArgs(TRUE)) Thanks, Brad _________________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/____search/mailinglists/ <http://galaxyproject.org/__search/mailinglists/> <http://galaxyproject.org/__search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>>
On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
The initial error now seems to be taken care of and now am getting this message on attempting to run tool:
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", line 109, in __init__ commands = initial_command.rstrip("; ") AttributeError: 'NoneType' object has no attribute 'rstrip'
This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ?
This is an important question :)
Also, please remember to CC the mailing list and not just reply to the previous email's sender only.
Thanks,
Peter
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
Error in value[[3L]](cond) :
failed to read experimental design data: cannot open the connection
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In file(file, "rt") : cannot open file 'NA': No such file or directory
Execution halted
On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
The initial error now seems to be taken care of and now am getting this message on attempting to run tool:
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 176, in build_command_line return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
line 19, in build_command commands_builder = CommandsBuilder(job_wrapper.get_command_line()) File
"/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
line 109, in __init__ commands = initial_command.rstrip("; ") AttributeError: 'NoneType' object has no attribute 'rstrip'
This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ?
This is an important question :)
Also, please remember to CC the mailing list and not just reply to the previous email's sender only.
Thanks,
Peter
This is not what I suggested, I said
Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output
replacing $genedata $pathwayid $species $output with meaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote:
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
Error in value[[3L]](cond) :
failed to read experimental design data: cannot open the connection
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In file(file, "rt") : cannot open file 'NA': No such file or directory
Execution halted
On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com mailto:p.j.a.cock@googlemail.com> wrote:
> On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_line = self.build_command_line( >> job_wrapper, include_metadata=include_metadata, >> include_work_dir_outputs=include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_metadata, >> include_work_dir_outputs=include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", >> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", >> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'
Error in grep(species, pathway.id) :
argument "pathway.id" is missing, with no default
Calls: pathview -> grep
Execution halted
On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
This is not what I suggested, I said
Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output
replacing $genedata $pathwayid $species $output with meaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote:
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
Error in value[[3L]](cond) :
failed to read experimental design data: cannot open the connection
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning message:
In file(file, "rt") : cannot open file 'NA': No such file or directory
Execution halted
On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com mailto:p.j.a.cock@googlemail.com> wrote:
> On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_line = self.build_command_line( >> job_wrapper, include_metadata=include_metadata, >> include_work_dir_outputs=include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_metadata, >> include_work_dir_outputs=include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", >> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py", >> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
Hi Brad
On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'
I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....."
I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing
You provide 3 arguments '/Users/bbelfio1/Documents/sample.txt', '04110', and 'HSA'
However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output
Error in grep(species, pathway.id http://pathway.id) :
argument "pathway.id http://pathway.id" is missing, with no default
Calls: pathview -> grep
Execution halted
As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy
Hans-Rudolf
On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/____init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command___line = self.build_command_line( >> job_wrapper, include_metadata=include___metadata, >> include_work_dir_outputs=__include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/____init__.py", >> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include___metadata, >> include_work_dir_outputs=__include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py", >> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.__get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py", >> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'
I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....."
I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing
You provide 3 arguments '/Users/bbelfio1/Documents/sample.txt', '04110', and 'HSA'
However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output
Error in grep(species, pathway.id http://pathway.id) :
argument "pathway.id http://pathway.id" is missing, with no default
Calls: pathview -> grep
Execution halted
As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy
Hans-Rudolf
On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and nowam getting this >> message on attempting to run tool: >> >> File
"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/____init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command___line = self.build_command_line( >> job_wrapper, include_metadata=include___metadata, >> include_work_dir_outputs=__include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/runners/____init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include___metadata, >> include_work_dir_outputs=__include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.__get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/__lib/galaxy/jobs/command___factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute'rstrip' >>
This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: > again, have you tried running your Rscript outside ofGalaxy called by > Rscript_wrapper.sh ? >
This is an important question :) Also, please remember to CC the mailing list and not justreply to the previous email's sender only.
Thanks, Peter
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py", >> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py", >> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
The XML file is: <tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id$species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output withmeaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in yourXML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf26.2@gmail.com wrote:
The XML file is:
<tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote: Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote: Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py", >> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py", >> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in your XML. On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
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Thank you for your patience and help, I removed the periods and am running into this error:
/bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: Permission denied
Does it have to do with the fact Im using SQLite and not Postgres?
On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blankenberg dan@bx.psu.edu wrote:
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf26.2@gmail.com wrote:
The XML file is:
<tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output withmeaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in yourXML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
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Never mind problem solved! Thanks again
On Tue, Apr 29, 2014 at 2:40 PM, Bradley Belfiore bradbelf26.2@gmail.comwrote:
Thank you for your patience and help, I removed the periods and am running into this error:
/bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: Permission denied
Does it have to do with the fact Im using SQLite and not Postgres?
On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blankenberg dan@bx.psu.eduwrote:
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore bradbelf26.2@gmail.com wrote:
The XML file is:
<tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output withmeaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in yourXML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
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: http://lists.bx.psu.edu/
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FWIW: looks like a trivial xml syntax error is in this line:
<command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output </command> .................*..............................*
There seem to be one too many ">" - the first one is probably a problem?
For the record, viewing your xml in firefox is sometimes very helpful for finding invalid xml which can otherwise be very hard to find.
On Wed, Apr 30, 2014 at 2:32 AM, Bradley Belfiore bradbelf26.2@gmail.comwrote:
The XML file is:
<tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output withmeaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in yourXML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
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: http://lists.bx.psu.edu/
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I am running into a problem with coloring of my KEGG image produced. When loading pathview and running this script in R:
pv.out<-pathview(gene.data=gse16873.d, pathway.id="04110", species="hsa", out.suffix="gse") you get an image with full coloration. With the same command in galaxy, the image produced has only white and red, Im wondering if this is a problem within my scripts or what may be causing this:
read<-read.delim(file <- gene.data, header=TRUE )
pv.out <- pathview(gene.data=read, pathway.id= pathway.id, species=species, out.suffix=out.suffix, kegg.native=T)
write.csv(pv.out$plot.data.gene, file=table)
file.rename(paste(species, pathway.id, ".", out.suffix, ".png", sep = ""), output)
Thanks,
Brad
On Tue, Apr 29, 2014 at 6:30 PM, Ross ross.lazarus@gmail.com wrote:
FWIW: looks like a trivial xml syntax error is in this line:
<command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output </command> .................*..............................*
There seem to be one too many ">" - the first one is probably a problem?
For the record, viewing your xml in firefox is sometimes very helpful for finding invalid xml which can otherwise be very hard to find.
On Wed, Apr 30, 2014 at 2:32 AM, Bradley Belfiore bradbelf26.2@gmail.comwrote:
The XML file is:
<tool id="pathview" name="pathview" version="1.0"> <description> Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.</description> <command> interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $ pathway.id $species $out.suffix $output </command> <inputs> <param name="gene.data" type="data" format="data" label="enter input file"/> <param name="pathway.id" type="text" format="text" label="Pathway ID"/> <param name="species" type="text" format="text" label="Species"/> <param name="out.suffix" type="text" format="text" label="Output Suffix" /> </inputs> <outputs> <data format="pdf" name="output"/> </outputs> </tool>
With basic Rscript : args <- commandArgs(TRUE) ## inputs gene.data <- args[1] pathway.id <- args[2] species <-args[3] out.suffix <-args[4] output <-args[5]
suppressMessages(library("pathview")) suppressMessages(library("KEGGgraph")) suppressMessages(library("Rgraphviz"))
pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id, species=species, out.suffix=output, kegg.native=T)
On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Brad
To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about:
Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job job_wrapper.prepare() File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7- macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch mailto:hrh@fmi.ch> wrote:
Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R '/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....." I don't see the word "Rscript_wrapper.sh" in your line, hence it does not correspond to the command galaxy is executing You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt', '04110', and 'HSA' However in an earlier mail you mention four arguments: $genedata $pathwayid $species $output Error in grep(species, pathway.id <http://pathway.id> <http://pathway.id>) : argument "pathway.id <http://pathway.id> <http://pathway.id>" is missing, with no default Calls: pathview -> grep Execution halted As long as you are not sure, whether your script is working on the command line the way you want it to be executed in Galaxy, there is no point in putting it into Galaxy Hans-Rudolf On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>> wrote: This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output withmeaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com> <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>> <mailto:p.j.a.cock@googlemail. <mailto:p.j.a.cock@googlemail.>____com <mailto:p.j.a.cock@googlemail.__com <mailto:p.j.a.cock@googlemail.com>>>> wrote: > On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py", >> line 153, in prepare_job >> job_wrapper.runner_command_____line = self.build_command_line( >> job_wrapper, include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
>> line 176, in build_command_line >> return build_command( self, job_wrapper, >> include_metadata=include_____metadata, >> include_work_dir_outputs=____include_work_dir_outputs ) >> File "/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 19, in build_command >> commands_builder = CommandsBuilder(job_wrapper.____get_command_line()) >> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",
>> line 109, in __init__ >> commands = initial_command.rstrip("; ") >> AttributeError: 'NoneType' object has no attribute 'rstrip' >> This is still breaking inside Galaxy, before ever trying to run your scripts. There is likely still a problem in yourXML.
On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch> <mailto:hrh@fmi.ch <mailto:hrh@fmi.ch>>>> wrote: > again, have you tried running your Rscript outside of Galaxy called by > Rscript_wrapper.sh ? > This is an important question :) Also, please remember to CC the mailing list and not just reply to the previous email's sender only. Thanks, Peter
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: http://lists.bx.psu.edu/
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On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
<command> interpreter="bash">Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command>
So I believe Im calling R via the Rscript_wrapper.sh?
There is a problem with the XML closing of the <command> tag. You appear to have a bash script calling an R script. Try:
<command interpreter="bash">Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command>
Or, if you mark your shell script as executable and include the #!/bin/bash line, you don't need the interpreter setting:
<command>Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command>
Also, you should be able to use relative paths rather than that absolute path (which is not portable).
Peter
galaxy-dev@lists.galaxyproject.org
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Bradley Belfiore -
Daniel Blankenberg -
Hans-Rudolf Hotz -
Peter Cock -
Ross