Hi Sarah, It seems that Chipmunk is not well executed (reason why it can't found the log file). I think that there's some ruby libraries missing. Please try to run ChIPMunk externally this way: ruby /path/to/ChIPMunk/run_chiphorde.rb If you receive this kind of error message, it means that it missed one library to work: ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- rexml/formatters/pretty (LoadError) from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in `require' from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 I already had the problem and the missing library was this one: http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pret... Tell me if it works.. ++, Alban -- Alban Lermine Unité 900: INSERM - Mines ParisTech - Institut Curie " Bioinformatics and Computational Systems Biology of Cancer" 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel: +33 (0) 1 56 24 69 84 Le 7 janv. 2013 à 17:13, Sarah Maman <sarah.maman@toulouse.inra.fr> a écrit :

Hello,

I 've integrated nebula suite in my local instance of galaxy but here is the error message received when running ChipMunk analysis : Galaxy cannot stat a file "_chiphorde.log" in the job working directory.

Do you have any idea ?

Thanks in advance, Sarah

<ChiMunk_Log.jpg>