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. Regards, Olivier. -----Message d'origine----- De : Peter Cock [mailto:p.j.a.cock@googlemail.com] Envoyé : vendredi 4 décembre 2015 15:17 À : Olivier CLAUDE <o.claude@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.claude@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: https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wo... (1) put runWolfPsortSummary somewhere where your cluster nodes and Galaxy can see it. I used the folder /opt/WoLFPSORT_package_v0.2/ meaning /opt/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary 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 ~/bin/runWolfPsortSummary $ 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) os.chdir("/opt/WoLFPSORT_package_v0.2/bin") args = ["./runWolfPsortSummary"] + sys.argv[1:] return_code = subprocess.call(args) os.chdir(saved_dir) sys.exit(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 ~/bin/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. Peter