I followed the instuctions given by peter and signalp works with galaxy!
Thanks a lot!
Do I try the same for tmhmm2 and promoter2?
Thanks a lot again!

Olivier


-----Message d'origine-----
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : jeudi 12 novembre 2015 16:36
À : Björn Grüning <bjoern.gruen...@gmail.com>
Cc : Olivier CLAUDE <o.cla...@outlook.fr>; galaxy-dev 
<galaxy-...@lists.bx.psu.edu>
Objet : Re: [galaxy-dev] Tmhmm and signal P

On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning <bjoern.gruen...@gmail.com> 
wrote:
> Hi,
>
> please make also sure the /bin directory inside of the signalp folder 
> is in your PATH.
>
> Things like combine-hmm-plp.awk should be included.
>
> Ciao,
> Bjoern

Thanks Bjorn,

You don't need put that on the path, alternatively you can edit the SIGNALP=... 
line near the start of the signalp script - it defaults to 
/usr/opt/signalp-3.0/bin

What we do is have a symbolic link (which is on the path) which points to the 
main script under /usr/opt/ or similar. These are my colleague's notes:

<quote>

SIGNALP arrives as the compressed file signalp-3.0.Linux.tar.Z, which can be 
uncompressed as usual:

$ tar -zxvf signalp-3.0.Linux.tar.Z

The resulting directory should be copied to /usr/opt/signalp-3.0 (this location 
is assumed by the SIGNALP scripts), and a symbolic link added to /usr/local/bin 
to enable command-line use. We also need to make the /usr/opt/signalp-3.0/tmp 
directory world-writable so that SIGNALP will run.

$ sudo cp -R signalp-3.0/ /usr/opt/
$ sudo ln -s /usr/opt/signalp-3.0/signalp /usr/local/bin $ sudo chmod 777 
/usr/opt/signalp-3.0/tmp

</quote>

If you don't have sudo rights, a little more work is needed. We currently use 
$HOME/opt/signalp-3.0/ and $HOME/bin/signalp as a symlink to 
/mnt/galaxy/opt/signalp-3.0/signalp but this requires you edit the script line 
to record the alternative path as the SIGNALP variable.

Peter
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