Everything is working fine now.
I experienced problems : I forgot to delete some files this made a conflict.
If anybody needs, the python script has to be in the bin folder of the computer 
not  in the HOME folder  (I've made a mistake with the tilde)
Thanks again, normally I will not bother you anymore Peter.



-----Message d'origine-----
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : vendredi 4 décembre 2015 15:17
À : Olivier CLAUDE <o.cla...@outlook.fr>
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> Ok i did not saw it.
> I runned it with ./ and it worked fine. It gave me the same answer you gave 
> me earlier.
> Olivier

Excellent :)

So, this matches what I found - as long as I changed to the Wolf PSORT 
directory first, runWolfPsortSummary worked OK.

If I just put the runWolfPsortSummary bin folder on the $PATH, then it failed.

Perhaps there is a small step in the instructions we both missed?

I suggest you try my workaround, which I linked to before:

(1) put runWolfPsortSummary somewhere where your cluster nodes and Galaxy can 
see it. I used the folder /opt/WoLFPSORT_package_v0.2/ meaning 
is the script itself.

Your folder ~/galaxy/CBS/WoLFPSort-master/ would be fine.

(2) Using a text editor (emacs, nano, vi, etc) create a new file named 
runWolfPsortSummary (without an extension) somewhere on your path, I suggest 

$ emacs ~/bin/runWolfPsortSummary

(3) Copy this into the ~/bin/runWolfPsortSummary file,

#!/usr/bin/env python
#Wrapper script to call WoLF PSORT from its own directory.
import os
import sys
import subprocess
saved_dir = os.path.abspath(os.curdir)
args = ["./runWolfPsortSummary"] + sys.argv[1:] return_code = 

(3) Mark this wrapper script as executable:

$ chmod a+x ~/bin/runWolfPsortSummary

(4) Check ~/bin is on your path, so that using runWolfPsortSummary (without a 
leading dot slash) will run the new wrapper script:

$ which runWolfPsortSummary

(5) Test the new wrapper script from some other directory, e.g.

$ cd ~
$ runWolfPsortSummary animal <~/galaxy/test-data/four_human_proteins.fasta

(6) If that all works, then the Galaxy wrapper should work too.

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