This is working! For signlaP and promoter at least.

I still got this weird error with tmhmm ("no output from tmhmm") and I can't 
figure what's wrong .

I experienced some problems at the beginning with signal and promoter, because 
I forgot to remove the path I've made in the .bashrc . They were broken in the 
If anybody experience the problem in the future, just remove the old ones, 
remove from the path the wrong one, and redo the command line.

Thanks a lot.

Do anybody knows where i can find WolFPSORT? The website semms to be down for a 
while now and I am not able to find it anywhere?

Thanks again!

Olivier .

-----Message d'origine-----
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : jeudi 12 novembre 2015 17:35
À : Olivier CLAUDE <o.cla...@outlook.fr>
Cc : Björn Grüning <bjoern.gruen...@gmail.com>; galaxy-dev 
Objet : Re: [galaxy-dev] Tmhmm and signal P

On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> 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

Our notes from installing tmhmm2:

TMHMM arrives as the compressed file tmhmm-2.0c.Linux.tar.gz which can be 
uncompressed in the usual way

$ tar -zxvf tmhmm-2.0c.Linux.tar.gz

We also move this to /usr/opt/timhmm-2.0c for consistency with SIGNALP, and 
create the link in /usr/local/bin:

$ sudo cp -R tmhmm-2.0c/ /usr/opt
$ sudo ln -s /usr/opt/tmhmm-2.0c/bin/tmhmm /usr/local/bin/

We needed to modify the main TMHMM script and tmhmmformat.pl to point it at the 
right Perl on the system, replace the first line:



#!/usr/bin/env perl

Also at about line 17, set the path to match what you've used:

$opt_basedir = '/usr/opt/tmhmm-2.0c';

You can change the defaults in this script too, but the Galaxy wrapper should 
not mind.

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