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 <bradbelf2...@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 <h...@fmi.ch> wrote:
> Hi Brad
>
> To me, this looks like an error in tool definition file (ie the xml file).
> Something like using $gene in the "command" tag without defining it in a
> "param" tag. But it is difficult to guess without seeing to full xml file.
>
>
> Regards Hans-Rudolf
>
>
> On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
> Upon going back over my script I got it working on the command line as
> suggested, and when attempting to execute in my instance of galaxy I got
> this error message which I was not sure about:
>
> Traceback (most recent call last):
> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 152, in prepare_job
> job_wrapper.prepare()
> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701,
> in prepare
> self.command_line = self.tool.build_command_line( param_dict )
> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line
> 2773, in build_command_line
> command_line = fill_template( self.command, context=param_dict )
> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in
> fill_template
> return str( Template( source=template_text, searchList=[context] ) )
> File
> "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py",
> line 1004, in __str__
> return getattr(self, mainMethName)()
> File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
> NotFound: cannot find 'gene'
>
>
>
> On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <h...@fmi.ch
> <mailto:h...@fmi.ch>> wrote:
>
> Hi Brad
>
>
>
> On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
>
> So upon doing what you suggested, I get:
>
> bravo:galaxy-dist bbelfio1$ 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 <h...@fmi.ch
> <mailto:h...@fmi.ch>
> <mailto:h...@fmi.ch <mailto:h...@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.c...@googlemail.com
> <mailto:p.j.a.c...@googlemail.com>
> <mailto:p.j.a.cock@googlemail.__com
> <mailto:p.j.a.c...@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.c...@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
> <h...@fmi.ch <mailto:h...@fmi.ch> <mailto:h...@fmi.ch
> <mailto:h...@fmi.ch>>
> <mailto:h...@fmi.ch <mailto:h...@fmi.ch>
> <mailto:h...@fmi.ch <mailto:h...@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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