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
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
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