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
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 integrationand 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)## inputsgene.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 $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
Upon going back over my script I got it working on the command line as
suggested, and when attempting to execute in my instance of galaxy I got
this error message which I was not sure about:
Traceback (most recent call last):
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job
job_wrapper.prepare()
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py", line 2773, in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
return getattr(self, mainMethName)()
File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <hrh@fmi.ch<mailto:hrh@fmi.ch>> wrote:/Users/bbelfio1/galaxy-dist/__tools/pathview/Pathview.R
Hi Brad
On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript
'/Users/bbelfio1/Documents/__sample.txt' '04110' 'HSA'You provide 3 arguments '/Users/bbelfio1/Documents/__sample.txt',
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
'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>This is not what I suggested, I said/Users/bbelfio1/galaxy-dist/____tools/pathview/Pathview.R
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<mailto:p.j.a.cock@googlemail.
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.>____com"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/runners/______init__.py",
<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
>> 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",>> include_metadata=include_____metadata,
>> line 176, in build_command_line
>> return build_command( self, job_wrapper,
>>
include_work_dir_outputs=____include_work_dir_outputs )
>> File
"/Users/bbelfio1/galaxy-dist/____lib/galaxy/jobs/command_____factory.py",CommandsBuilder(job_wrapper.____get_command_line())
>> line 19, in build_command
>> commands_builder =
>> 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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