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

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 /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)
args = ["./runWolfPsortSummary"] + sys.argv[1:]
return_code = subprocess.call(args)

(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.

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:

To search Galaxy mailing lists use the unified search at:

Reply via email to