On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <o.cla...@outlook.fr> wrote:
> Hello,
>
> This is working! For signlaP and promoter at least.
>

Good.

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

The message "no output from tmhmm" is from my wrapper script,
https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/tmhmm2.py

This can be triggered when tmhmm silently fails, e.g. you have
just the 32bit binaries on a 64bit system:

https://github.com/peterjc/pico_galaxy/commit/e79bc01a6e3ef68d21e0921cd65cd23d7e1f7728

Can you run tmhmm successfully outside of Galaxy?

> 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 .

Yes, http://wolfpsort.org/ is still down (and has been for some months
so this is not a temporary glitch). The best plan would be to try to
get in touch with Paul Horton. I will try to email him (and CC you).

I do have a copy of WoLF PSORT v0.2 but this is not an open source
tool, and redistribution is restricted. Assuming you want it for
academic use only (so no commercial part-funding, no industry
partnership, etc) than I can probably forward it to you off list.

Peter

--

WoLF PSORT Package Command Line Version 0.2 License
Author: Paul Horton
Copyright: All Rights Reserved
Created: 2005/9/1
Last Modified: 2005/9/1


LICENSE

1. Academic License

If you are an academic you may freely use this package on site or
redistribute it for academic use as is. This does not include
providing a WoLF PSORT prediction service over the internet.  Academic
citation would be highly appreciated.

Non-profit use is a necessary condition for "academic". If in doubt
please contact Paul Horton.


2. Commercial License

Any rights not explicitly given in this license are reserved. However,
any potential users are encouraged to contact Paul Horton to discuss
other licensing arrangements.
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