On Fri, Dec 4, 2015 at 2:16 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
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)
Sorry, you'd need to change the change director line to match your setup. You can't use the tilde (~) or $HOME here, so something like this I guess: os.chdir("/home/xxxxx/galaxy/CBS/WoLFPSort-master/")
(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
I filed this as an issue on the GitHub mirror: https://github.com/fmaguire/WoLFPSort/issues/1 Peter