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 .. <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@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@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@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_@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/)%C2%A0 216-392-3087 Ontario Institute for Cancer Research
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at: