To unpack this mystery, you need to follow the chain from
tool_conf.xml (that's what the tool menu is made from) to the actual
tool directory and xml file name - eg:
rerla@rosst61:~/rgalaxy$ grep -i group tool_conf.xml
..
..
That means you need to look in [galaxyroot]/tools/stats for
grouping.xml to understand what the tool menu entry is going to do.
The actual command is found in the first few lines of the tool xml file:
rerla@rosst61:~/rgalaxy$ head tools/stats/grouping.xml
data by a column and perform aggregate operation on
other columns.
grouping.py
$out_file1
so the python script you want is in /tools/stats/grouping.py - I'd be
surprised if that's AWOL from a fresh mercurial clone?
Now for the harder part: unfortunately the error message was missing,
but my first guess is that your Python does not (yet) have rpy
installed.
There's a slew of dependencies described at
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
I hope this helps?
On Mon, Apr 18, 2011 at 11:14 AM, Scott Cain wrote:
> Hi Peter,
>
> I can't help you with that, so I'm going to forward this to the
> galaxy-user mailing list, galaxy-user@lists.bx.psu.edu, where
> presumably someone will know the answer.
>
> Scott
>
>
> On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge
> wrote:
>>
>> Hi, I have configured Galaxy on my desktop and it appears to be running
>> fine. However, I suspect that I am missing tools from the galaxy-dist/tools.
>> When I try to run the 'group' command from the join, subtract and group tab
>> I get this error below:
>>
>>
>>
>>
>> And when I look in my computers directory (galaxy-dist/tools) for the py
>> scripts there isn't a script for 'join, subtract and group'. This is also
>> the case for Graph/Display data. Thus, when I try to run Graph/display data
>> I get the same error. How can I rectify this? I configured the Galaxy suite
>> yesterday, following the on-line Galaxy tutorial. Is it possible for
>> somebody to forward the relevant py scripts for my to place in my
>> galaxy-dist/tools directory.
>>
>> I look forward to hearing your advice,
>> Pete
>>
>
>
>
> --
>
> Scott Cain, Ph. D. scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___
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at usegalaxy.org. Please keep all replies on the list by
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