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
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
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
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
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
On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz h...@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=bashRscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid
The initial error now seems to be taken care of and now am getting this
message on attempting to run tool:
File /Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line 153, in prepare_job
job_wrapper.runner_command_line = self.build_command_line(
job_wrapper,
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ 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
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
