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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