On Fri, Nov 13, 2015 at 11:08 AM, Peter Cock wrote:
> On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE wrote:
>>
>> 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, h
Thnks for WolFPSORT,
I have to check with my PI because we are uder the administrative supervision
of 2 big public structures with very particular rules...
About Tmhmm, it works. I've restarted galaxy, then the station and now
everythings semms to be ok.
Thank you for your time & help!
Olivier
On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE 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
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
Cc : Björn Grüning ; galaxy-dev
Objet : Re: [galaxy-dev] Tmhmm and signal P
On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE 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
üning
Cc : Olivier CLAUDE ; galaxy-dev
Objet : Re: [galaxy-dev] Tmhmm and signal P
On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning
wrote:
> Hi,
>
> please make also sure the /bin directory inside of the signalp folder
> is in your PATH.
>
> Things like combine-hmm-plp
On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning
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
x27;Peter Cock'
>
> Cc : 'Björn Grüning' ; 'galaxy-dev'
>
> Objet : Re: [galaxy-dev] Tmhmm and signal P
>
> Hi,
>
> please make also sure the /bin directory inside of the signalp folder is in
> your PATH.
>
> Things like combine-hmm-pl
---Message d'origine-
De : Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Envoyé : jeudi 12 novembre 2015 15:56
À : Olivier CLAUDE ; 'Peter Cock'
Cc : 'Björn Grüning' ; 'galaxy-dev'
Objet : Re: [galaxy-dev] Tmhmm and signal P
Hi,
please make also sure the /bin
ith your personal account?
>> They probably have different $PATH settings.
>
> I have only one account one this machine. Is Galaxy considered as another
> user?
> I installed it as a simple user, to avoid all the problems with the rights
> with the root.
>
> Thanks aga
On Thu, Nov 12, 2015 at 2:14 PM, Olivier CLAUDE wrote:
> Hi Peter,
>
> I totally agree with you about the CBS, i had so much problems to get the
> files, there are so many restrictions with my university mails.
>
> ...
> My email editor changed "signalp" in"Signalp" and in"signal" in my previous
one this machine. Is Galaxy considered as another user?
I installed it as a simple user, to avoid all the problems with the rights with
the root.
Thanks again,
Olivier
-Message d'origine-----
De : Peter Cock [mailto:p.j.a.c...@googlemail.com]
Envoyé : jeudi 12 novembre 2015 14:22
Hi Olivier,
On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE wrote:
> Hi Björn!
>
> I do have signalP 3 , it's installed and on the path.
Good. It is a shame that CBS use a proprietary license which forbids
redistribution and packaging - otherwise I could have tried to automate
this.
> The tests
ovembre 2015 12:48
À : Olivier CLAUDE
Cc : 'galaxy-dev'
Objet : Re: [galaxy-dev] Tmhmm and signal P
Hi Olivier,
you need to have signalp in version 3.
You have installed it already and it is now on your $PATH?
> Signal P: with v3.0: it can’t localize it (signal not found) (I can’t
Hi Olivier,
you need to have signalp in version 3.
You have installed it already and it is now on your $PATH?
> Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even
> launch it in command line)
What is the error if you run it on command line?
Ciao,
Bjoern
>
>
Hello,
I am installing this package from peterjc.
I downloaded the tools from the CBS but i can’t run it in galaxy :
TMHMM : galaxy gives the error : no output from tmhmm2
Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even
launch it in command line)
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