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

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

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

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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Never mind problem solved! Thanks again On Tue, Apr 29, 2014 at 2:40 PM, Bradley Belfiore <bradbelf26.2@gmail.com>wrote:

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 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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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.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

___________________________________________________________ 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/