Is gnuplot installed?

Am 12.11.2015 um 16:23 schrieb Olivier CLAUDE:
> Hello again,
> 
> I have put the /signalp-3.0/bin in the path and it changed the error message 
> to :
> "error running /usr/bin/gnuplot on 
> <path>/signal-3.0/tmp/TMP15....31945/plot.gnu"
> 
> I have restarted galaxy tried the same search, no changes in the output.
> 
> Any idea for tmhmm also?
> 
> 
> 
> 
> -----Message d'origine-----
> De : Björn Grüning [mailto:bjoern.gruen...@gmail.com] 
> Envoyé : jeudi 12 novembre 2015 15:56
> À : Olivier CLAUDE <o.cla...@outlook.fr>; 'Peter Cock' 
> <p.j.a.c...@googlemail.com>
> Cc : 'Björn Grüning' <bjoern.gruen...@gmail.com>; 'galaxy-dev' 
> <galaxy-...@lists.bx.psu.edu>
> 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-plp.awk should be included.
> 
> Ciao,
> Bjoern
> 
> Am 12.11.2015 um 15:14 schrieb Olivier CLAUDE:
>> 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.
>>
>>> That's not right - the case is all inconsistent. The binary name signalp is 
>>> all lower case, so if gawk, but I infer you had something like this:
>>> $ signalp -G -t euk does_not_exist.faa
>>> gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot 
>>> open file `does_not_exist.faa' for reading (No such file or 
>>> directory)
>>> signalp: ERROR in sequence file(s), check syntax
>>
>> For the "$SIGNALP" I just wrote what was written in the readme file, 
>> If I open the "signalp" file, I can see on line 17 
>> "SIGNALP=<path>/signal-3.0"
>> I assume that when I writ $SIGNALP it refers to this path?
>> My email editor changed "signalp" in"Signalp" and in"signal" in my 
>> previous message :'(
>>
>>> Which folder were you in, and did the test/test.seq file exist relative to 
>>> it?
>>
>> I was in "~/signal-3.0" and the file "/test/test.seq" exists. I kept the 
>> structure from the archive, I did not wanted to change everything.
>>
>>
>>> But in any case, good news that signalp appears to be on your $PATH
>>
>> I had to write in in the .bashrc of my account otherwise I had to export it 
>> everytime.
>>
>>> I'm guessing there is another copy-and-paste error here, with "signal" 
>>> rather than "signalp". Perhaps your email editor is being too helpful with 
>>> auto-correction?
>>
>> I just checked and yes it seems that he is too helpful.
>>
>>> When you ran signalp at the command line by hand, were you doing it as the 
>>> Galaxy Linux user, or with 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 again,
>>
>> Olivier
>>
>>
>>
>> -----Message d'origine-----
>> De : Peter Cock [mailto:p.j.a.c...@googlemail.com]
>> Envoyé : jeudi 12 novembre 2015 14:22
>> 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
>>
>> Hi Olivier,
>>
>> On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.cla...@outlook.fr> 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 files are the ones from the archive (no changes nor I tried 
>>> to open it manually)
>>>
>>> The exact lines in the prompt are:
>>>
>>> $SIGNALP
>>> Signalp -G  -t euk test/test.seq
>>> Gawk: fatal: cannot open file 'test/test.seq' for reading (no such 
>>> file or directory)
>>> Signal: ERROR in sequence file(s), check syntax
>>
>> That's not right - the case is all inconsistent. The binary name signalp is 
>> all lower case, so if gawk, but I infer you had something like this:
>>
>> $ signalp -G -t euk does_not_exist.faa
>> gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot 
>> open file `does_not_exist.faa' for reading (No such file or directory)
>> signalp: ERROR in sequence file(s), check syntax
>>
>> Which folder were you in, and did the test/test.seq file exist relative to 
>> it?
>>
>> But in any case, good news that signalp appears to be on your $PATH
>>
>>> In galaxy report :
>>>
>>> Fatal error : exit code 127 ()
>>> /bin/sh: 1 : signal: not found
>>> One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
>>> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > 
>>> <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:
>>>
>>
>> I'm guessing there is another copy-and-paste error here, with "signal" 
>> rather than "signalp". Perhaps your email editor is being too helpful with 
>> auto-correction?
>>
>> When you ran signalp at the command line by hand, were you doing it as the 
>> Galaxy Linux user, or with your personal account?
>> They probably have different $PATH settings.
>>
>>>
>>> That's all.
>>> Thank you for your help again .
>>>
>>> Olivier.
>>
>> Thanks Bjoern :)
>>
>> Peter
>>
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