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.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: https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/wolf_psort.py#L43 (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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
