Hi,

You have to use ChIPMunk v2 with Nebula (I don't think its compatible with the 
v3)

++,

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 8 janv. 2013 à 10:10, Sarah Maman <sarah.ma...@toulouse.inra.fr> a écrit :

> 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.genop...@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.genop...@toulouse.inra.fr
>>>>> 07.01.2013 14:35 - sarah.ma...@toulouse.inra.fr a écrit:
>>>>> 
>>>>>   
>>>>>       
>>>>>> A user filled out the contact form on bioinfo.genotoul.fr.
>>>>>> 
>>>>>> 
>>>>>> ###master_email-line-plain_mailsubject##
>>>>>> 
>>>>>> E-Mail: sarah.ma...@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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ---------------------------------- This message was created 
>>>>>> automatically.
>>>>>>     
>>>>>>         
>>>>> --------------------------------
>>>>> 
>>>>> 
>>>>> 
>>>>>  
>>>>> 
>>>>>   
>>>>>       
>>>>     
>>> 
>>> 
>>> 
>>>  
>>> 
>>>   
>> 
> 

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