[galaxy-user] [Gmod-help] Missing tools in my configured galaxy

[Ross]

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 at rosst61:~/rgalaxy$ grep -i group tool_conf.xml
..
    <tool file="stats/grouping.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 at rosst61:~/rgalaxy$ head tools/stats/grouping.xml
<tool id="Grouping1" name="Group" version="1.9.4">
  <description>data by a column and perform aggregate operation on
other columns.</description>
  <command interpreter="python">
    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 <scott at scottcain.net> 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 at lists.bx.psu.edu, where
> presumably someone will know the answer.
>
> Scott
>
>
> On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge <peter_tonge_ at hotmail.com> 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;