Thanks to Marie-Stephane to have found that this error is due to a diifference of verion.
Alban, could you please tell us which version (2 or 3) do you use in your Galaxy tools, in order to install this version on our cluster ?
Thanks in advance,
Sarah



Sarah Maman a écrit :

Thanks Alban for your answer,

Our admin system has tested to run ChIPMunk externally but didn't received the same error message.
In fact, pretty.rb lib is found.
It seems to be a difference between chiphorde version : we have run_chiphorde4.rb  instead of  run_chiphorde.rb
Do you think that we have to install your version or thaht we just need to rename some files?

Your error message when running ruby run_chiphorde4.rb is :

LLIB 08 Jan 09:10:17 [ytilib]	ytilib required, working directory
/usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts
LLIB 08 Jan 09:10:17 [ytilib]	use_chiphorde4.rb started, usage <motif_template>
<ChIPHorde-engine-params>
LLIB 08 Jan 09:10:17 [ytilib]	run_chiphorde4.rb

Thanks in advance,
Sarah


Support a écrit :

Bonjour,

Voilà ce que j'obtiens quand je lance la commande qu'il demande:

ruby run_chiphorde4.rb
LLIB 08 Jan 09:10:17 [ytilib]	ytilib required, working directory
/usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts
LLIB 08 Jan 09:10:17 [ytilib]	use_chiphorde4.rb started, usage <motif_template>
<ChIPHorde-engine-params>
LLIB 08 Jan 09:10:17 [ytilib]	run_chiphorde4.rb

Je n'obtiens donc pas l'erreur dont il parle.
Par ailleurs voici le chemin de la librairie:
/usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver.

Je continue à chercher avec ce que tu m'as envoyé.
Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils
aient renommé les fichiers


Cordialement,

Marie-Stephane Trotard

Génopole - Plateforme bio-informatique
Centre INRA de Toulouse - Unité de BIA
Chemin de Borde-Rouge - AUZEVILLE
BP 52627 - 31326 CASTANET-TOLOSAN CEDEX
tél. : +33 (0)5 61 28 54 27
Support : support.genopole@toulouse.inra.fr
08.01.2013 09:05 - Sarah Maman a écrit:

  

Bonjour Marie-Stephane,

A priori, il manquerait une librairie :

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


Merci d'avance,
Sarah


Support a écrit :
    

Bonjour,

Il me semble que je l'avais installé en même temps que FindPeaks:

/usr/local/bioinfo/src/ChIPMunk/current

Parles-tu d'un autre logiciel? D'un version?


Cordialement,

Marie-Stephane Trotard

Génopole - Plateforme bio-informatique
Centre INRA de Toulouse - Unité de BIA
Chemin de Borde-Rouge - AUZEVILLE
BP 52627 - 31326 CASTANET-TOLOSAN CEDEX
tél. : +33 (0)5 61 28 54 27
Support : support.genopole@toulouse.inra.fr
07.01.2013 14:35 - sarah.maman@toulouse.inra.fr a écrit:

  
      

A user filled out the contact form on bioinfo.genotoul.fr.


###master_email-line-plain_mailsubject##

E-Mail: sarah.maman@toulouse.inra.fr


Priority: Very low


Your Message: Bonjour,

Il me semble, sauf erreur de ma part, que ChipMunk n est pas installé sur
        

Genotoul.
  

Est-il possible, s il vous plaît, de l installer.

TrÚs cordialement,
Sarah Maman



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