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Question: Re: [Gmod-Help] Missing Tools In My Configured Galaxy
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gravatar for Scott Cain
7.6 years ago by
Scott Cain • 100
Scott Cain • 100 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 -- Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
gmod • 1.2k views
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modified 7.6 years ago by fubar ♦ 1.1k • written 7.6 years ago by Scott Cain • 100
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gravatar for fubar
7.6 years ago by
fubar ♦ 1.1k
Australia
fubar ♦ 1.1k wrote:
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> 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? -- 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;
ADD COMMENT • link written 7.6 years ago by fubar ♦ 1.1k
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