On Thu, Nov 12, 2015 at 2:14 PM, Olivier CLAUDE <o.claude@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? Regards, Peter