On Fri, Dec 4, 2015 at 2:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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)
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
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