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

___________________________________________________________
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/