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.

> That's not right - the case is all inconsistent. The binary name signalp is 
> all lower case, so if gawk, but I infer you had something like this:
>$ signalp -G -t euk does_not_exist.faa
>gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot open file 
>`does_not_exist.faa' for reading (No such file or directory)
>signalp: ERROR in sequence file(s), check syntax

For the "$SIGNALP" I just wrote what was written in the readme file,
If I open the "signalp" file, I can see on line 17 "SIGNALP=<path>/signal-3.0"
I assume that when I writ $SIGNALP it refers to this path?
My email editor changed "signalp" in"Signalp" and in"signal" in my previous 
message :'(

>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.


>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.

>I'm guessing there is another copy-and-paste error here, with "signal" rather 
>than "signalp". Perhaps your email editor is being too helpful with 
>auto-correction?

I just checked and yes it seems that he is too helpful.

>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.

Thanks again,

Olivier



-----Message d'origine-----
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : jeudi 12 novembre 2015 14:22
À : Olivier CLAUDE <o.cla...@outlook.fr>
Cc : Björn Grüning <bjoern.gruen...@gmail.com>; galaxy-dev 
<galaxy-...@lists.bx.psu.edu>
Objet : Re: [galaxy-dev] Tmhmm and signal P

Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> Hi Björn!
>
> I do have signalP 3 , it's installed and on the path.

Good. It is a shame that CBS use a proprietary license which forbids 
redistribution and packaging - otherwise I could have tried to automate this.

> The tests files are the ones from the archive (no changes nor I tried 
> to open it manually)
>
> The exact lines in the prompt are:
>
> $SIGNALP
> Signalp -G  -t euk test/test.seq
> Gawk: fatal: cannot open file 'test/test.seq' for reading (no such 
> file or directory)
> Signal: ERROR in sequence file(s), check syntax

That's not right - the case is all inconsistent. The binary name signalp is all 
lower case, so if gawk, but I infer you had something like this:

$ signalp -G -t euk does_not_exist.faa
gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot open file 
`does_not_exist.faa' for reading (No such file or directory)
signalp: ERROR in sequence file(s), check syntax

Which folder were you in, and did the test/test.seq file exist relative to it?

But in any case, good news that signalp appears to be on your $PATH

> In galaxy report :
>
> Fatal error : exit code 127 ()
> /bin/sh: 1 : signal: not found
> One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > 
> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:
>

I'm guessing there is another copy-and-paste error here, with "signal" rather 
than "signalp". Perhaps your email editor is being too helpful with 
auto-correction?

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.

>
> That's all.
> Thank you for your help again .
>
> Olivier.

Thanks Bjoern :)

Peter
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