e 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
> wrote:
>
>> The XML file is:
&
Never mind problem solved! Thanks again
On Tue, Apr 29, 2014 at 2:40 PM, Bradley Belfiore 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:
> Pe
Blankenberg 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
> wrote:
>
> The XML file is:
>
> Pathview is a t
8, 2014 at 12:07 PM, Hans-Rudolf Hotz 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/Pathvi
ol 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, Bradle
s $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/
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 wrote:
> > On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
> >>
> >> The initial error
;
>
> 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 $pathwayid $spec
I am new to galaxy and while trying to convert an R tool to a Galaxy usable
tool I keep getting: /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R:
line 1: syntax error near unexpected token `('
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any h
