On Thu, Nov 12, 2015 at 2:14 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> Hi Peter,
> I totally agree with you about the CBS, i had so much problems to get the 
> files, there are so many restrictions with my university mails.
> ...
> My email editor changed "signalp" in"Signalp" and in"signal" in my previous 
> message :'(

That makes sense :)

>>Which folder were you in, and did the test/test.seq file exist relative to it?
> I was in "~/signal-3.0" and the file "/test/test.seq" exists. I kept the 
> structure from the archive, I did not wanted to change everything.

Something is wrong if signalp could not open the test sequence file.

>>But in any case, good news that signalp appears to be on your $PATH
> I had to write in in the .bashrc of my account otherwise I had to export it 
> everytime.

Yes, I do something similar.

>>When you ran signalp at the command line by hand, were you doing it as the 
>>Galaxy Linux user, or with your personal account?
>>They probably have different $PATH settings.
> I have only one account one this machine. Is  Galaxy considered as another 
> user?
> I installed it as a simple user, to avoid all the problems with the rights 
> with the root.

Normally for a shared Galaxy server there would be a separate Linux
account just for Galaxy, there is probably something about this on the
wiki but I can't find a relevant link to share with your right now.

In your case it sounds like you run Galaxy under your own Linux account.
Have you restarted Galaxy since changing the $PATH setting?


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