Question: Re: Nebula Suite / _Chiphorde.Log Not Found
0
alermine • 40 wrote:
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 ŕ 17:13, Sarah Maman <sarah.maman@toulouse.inra.fr> a
écrit :