Hello,
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
/usr/local/bin
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
<galaxy-...@lists.bx.psu.edu>
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/local/bin/perl
with:
#!/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.
Peter
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