Question: Re: [Gmod-Help] Missing Tools In My Configured Galaxy
gravatar for Scott Cain
7.6 years ago by
Scott Cain100
Scott Cain100 wrote:
Hi Peter, I can't help you with that, so I'm going to forward this to the galaxy-user mailing list,, where presumably someone will know the answer. Scott -- Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (                     216-392-3087 Ontario Institute for Cancer Research
gmod • 1.2k views
ADD COMMENTlink modified 7.6 years ago by fubar1.1k • written 7.6 years ago by Scott Cain100
gravatar for fubar
7.6 years ago by
fubar1.1k 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> $out_file1 .... so the python script you want is in /tools/stats/ - 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 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 COMMENTlink written 7.6 years ago by fubar1.1k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour