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/Pretty.html
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.ma...@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>
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