Tmhmm and signal P

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Tmhmm and signal P

Olivier CLAUDE

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)

                With v4.1 it can’t be reached by galaxy (I am thinking about something with the name 3.0 vs 4.1 but I can’t figure where I have to change …)

 

 

Do anybody have an idea?

 

Regards,

 

 

M Olivier CLAUDE- PhD Student

INSERM/UPMC UMRS ICAN 1166 – Equipe 2

Faculté de médecine Pitié-Salpêtrière

91, bld de l'Hôpital - 3ème étage - Porte 305

75013 Paris

 

 


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Re: Tmhmm and signal P

Björn Grüning-3
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

>
>                 With v4.1 it can’t be reached by galaxy (I am thinking about something with the name 3.0 vs 4.1 but I can’t figure where I have to change …)
>
>  
>
>  
>
> Do anybody have an idea?
>
>  
>
> Regards,
>
>  
>
>  
>
> M Olivier CLAUDE- PhD Student
>
> INSERM/UPMC UMRS ICAN 1166 – Equipe 2
>
> Faculté de médecine Pitié-Salpêtrière
>
> 91, bld de l'Hôpital - 3ème étage - Porte 305
>
> 75013 Paris
>
>  
>
>  
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: Tmhmm and signal P

Olivier CLAUDE
Hi Björn!

I do have signalP 3 , it's installed and on the path.

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

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:


That's all.
Thank you for your help again .

Olivier.



-----Message d'origine-----
De : Björn Grüning [mailto:[hidden email]]
Envoyé : jeudi 12 novembre 2015 12:48
À : Olivier CLAUDE <[hidden email]>
Cc : 'galaxy-dev' <[hidden email]>
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
> even launch it in command line)

What is the error if you run it on command line?

Ciao,
Bjoern

>
>                 With v4.1 it can’t be reached by galaxy (I am thinking
> about something with the name 3.0 vs 4.1 but I can’t figure where I
> have to change …)
>
>  
>
>  
>
> Do anybody have an idea?
>
>  
>
> Regards,
>
>  
>
>  
>
> M Olivier CLAUDE- PhD Student
>
> INSERM/UPMC UMRS ICAN 1166 – Equipe 2
>
> Faculté de médecine Pitié-Salpêtrière
>
> 91, bld de l'Hôpital - 3ème étage - Porte 305
>
> 75013 Paris
>
>  
>
>  
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other
> Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Tmhmm and signal P

Peter Cock
Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <[hidden email]> 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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Re: Tmhmm and signal P

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:[hidden email]]
Envoyé : jeudi 12 novembre 2015 14:22
À : Olivier CLAUDE <[hidden email]>
Cc : Björn Grüning <[hidden email]>; galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Tmhmm and signal P

Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <[hidden email]> 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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Re: Tmhmm and signal P

Peter Cock
On Thu, Nov 12, 2015 at 2:14 PM, Olivier CLAUDE <[hidden email]> 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 message :'(

That makes sense :)

>>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.
>

Something is wrong if signalp could not open the test sequence file.

>
>>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.
>

Yes, I do something similar.

>>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.

Normally for a shared Galaxy server there would be a separate Linux
account just for Galaxy, there is probably something about this on the
wiki but I can't find a relevant link to share with your right now.

In your case it sounds like you run Galaxy under your own Linux account.
Have you restarted Galaxy since changing the $PATH setting?

Regards,

Peter
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in your mail client.  To manage your subscriptions to this
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Re: Tmhmm and signal P

Björn Grüning-3
In reply to this post by Olivier CLAUDE
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:[hidden email]]
> Envoyé : jeudi 12 novembre 2015 14:22
> À : Olivier CLAUDE <[hidden email]>
> Cc : Björn Grüning <[hidden email]>; galaxy-dev <[hidden email]>
> Objet : Re: [galaxy-dev] Tmhmm and signal P
>
> Hi Olivier,
>
> On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <[hidden email]> 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
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: Tmhmm and signal P

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:[hidden email]]
Envoyé : jeudi 12 novembre 2015 15:56
À : Olivier CLAUDE <[hidden email]>; 'Peter Cock' <[hidden email]>
Cc : 'Björn Grüning' <[hidden email]>; 'galaxy-dev' <[hidden email]>
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:[hidden email]]
> Envoyé : jeudi 12 novembre 2015 14:22
> À : Olivier CLAUDE <[hidden email]> Cc : Björn Grüning
> <[hidden email]>; galaxy-dev <[hidden email]>
> Objet : Re: [galaxy-dev] Tmhmm and signal P
>
> Hi Olivier,
>
> On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <[hidden email]> 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
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Tmhmm and signal P

Björn Grüning-3
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:[hidden email]]
> Envoyé : jeudi 12 novembre 2015 15:56
> À : Olivier CLAUDE <[hidden email]>; 'Peter Cock' <[hidden email]>
> Cc : 'Björn Grüning' <[hidden email]>; 'galaxy-dev' <[hidden email]>
> 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:[hidden email]]
>> Envoyé : jeudi 12 novembre 2015 14:22
>> À : Olivier CLAUDE <[hidden email]> Cc : Björn Grüning
>> <[hidden email]>; galaxy-dev <[hidden email]>
>> Objet : Re: [galaxy-dev] Tmhmm and signal P
>>
>> Hi Olivier,
>>
>> On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <[hidden email]> 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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Re: Tmhmm and signal P

Peter Cock
In reply to this post by Björn Grüning-3
On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning
<[hidden email]> 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 can edit the
SIGNALP=... line near the start of the signalp script - it defaults to
/usr/opt/signalp-3.0/bin

What we do is have a symbolic link (which is on the path) which points
to the main script under /usr/opt/ or similar. These are my
colleague's notes:

<quote>

SIGNALP arrives as the compressed file signalp-3.0.Linux.tar.Z, which
can be uncompressed as usual:

$ tar -zxvf signalp-3.0.Linux.tar.Z

The resulting directory should be copied to /usr/opt/signalp-3.0 (this
location is assumed by the SIGNALP scripts), and a symbolic link added
to /usr/local/bin to enable command-line use. We also need to make the
/usr/opt/signalp-3.0/tmp directory world-writable so that SIGNALP will
run.

$ sudo cp -R signalp-3.0/ /usr/opt/
$ sudo ln -s /usr/opt/signalp-3.0/signalp /usr/local/bin
$ sudo chmod 777 /usr/opt/signalp-3.0/tmp

</quote>

If you don't have sudo rights, a little more work is needed. We
currently use $HOME/opt/signalp-3.0/ and $HOME/bin/signalp as a
symlink to /mnt/galaxy/opt/signalp-3.0/signalp but this requires you
edit the script line to record the alternative path as the SIGNALP
variable.

Peter
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Re: Tmhmm and signal P

Olivier CLAUDE
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


-----Message d'origine-----
De : Peter Cock [mailto:[hidden email]]
Envoyé : jeudi 12 novembre 2015 16:36
À : Björn Grüning <[hidden email]>
Cc : Olivier CLAUDE <[hidden email]>; galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Tmhmm and signal P

On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning <[hidden email]> 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 can edit the SIGNALP=... line near the start of the signalp script - it defaults to /usr/opt/signalp-3.0/bin

What we do is have a symbolic link (which is on the path) which points to the main script under /usr/opt/ or similar. These are my colleague's notes:

<quote>

SIGNALP arrives as the compressed file signalp-3.0.Linux.tar.Z, which can be uncompressed as usual:

$ tar -zxvf signalp-3.0.Linux.tar.Z

The resulting directory should be copied to /usr/opt/signalp-3.0 (this location is assumed by the SIGNALP scripts), and a symbolic link added to /usr/local/bin to enable command-line use. We also need to make the /usr/opt/signalp-3.0/tmp directory world-writable so that SIGNALP will run.

$ sudo cp -R signalp-3.0/ /usr/opt/
$ sudo ln -s /usr/opt/signalp-3.0/signalp /usr/local/bin $ sudo chmod 777 /usr/opt/signalp-3.0/tmp

</quote>

If you don't have sudo rights, a little more work is needed. We currently use $HOME/opt/signalp-3.0/ and $HOME/bin/signalp as a symlink to /mnt/galaxy/opt/signalp-3.0/signalp but this requires you edit the script line to record the alternative path as the SIGNALP variable.

Peter
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Run workflow button does NOT gray-out when clicked -- causing big problems in long running workflow. Execute button does gray-out

ROBERT BROWN
In reply to this post by Björn Grüning-3
Good morning Team,
Could you please fix the "Run workflow" button that does NOT gray-out when clicked?   This causes my users to double-click it and then major issues.
Attached is the problem button, and two other "Execute" buttons that work correctly -- one also involved in workflows.
Thanks
bob brown

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Inital run of a workflow in Galaxy -- use Run workflow button doesNOT gray-out.png (55K) Download Attachment
Run on tool in Galaxy -- uses Execute button does gray-out.png (60K) Download Attachment
Rerun Workflow by starting from previous run History -- click rerun uses Execute button.png (91K) Download Attachment
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Re: Tmhmm and signal P

Peter Cock
In reply to this post by Olivier CLAUDE
On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE <[hidden email]> 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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Re: Run workflow button does NOT gray-out when clicked -- causing big problems in long running workflow. Execute button does gray-out

Nicola Soranzo-2
In reply to this post by ROBERT BROWN
Hi Bob,
I'd suggest you to open an issue at https://github.com/galaxyproject/galaxy/issues/new

Cheers,
Nicola

On 12/11/15 16:29, [hidden email] wrote:
Good morning Team,
Could you please fix the "Run workflow" button that does NOT gray-out when clicked?   This causes my users to double-click it and then major issues.
Attached is the problem button, and two other "Execute" buttons that work correctly -- one also involved in workflows.
Thanks
bob brown


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Re: Tmhmm and signal P

Olivier CLAUDE
In reply to this post by Peter Cock
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:[hidden email]]
Envoyé : jeudi 12 novembre 2015 17:35
À : Olivier CLAUDE <[hidden email]>
Cc : Björn Grüning <[hidden email]>; galaxy-dev <[hidden email]>
Objet : Re: [galaxy-dev] Tmhmm and signal P

On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE <[hidden email]> 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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Re: Tmhmm and signal P

Peter Cock
On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <[hidden email]> 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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Re: Tmhmm and signal P

Olivier CLAUDE
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 <[hidden email]> 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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in your mail client.  To manage your subscriptions to this
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Re: Tmhmm and signal P

Peter Cock
In reply to this post by Peter Cock
On Fri, Nov 13, 2015 at 11:08 AM, Peter Cock <[hidden email]> wrote:

> On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <[hidden email]> 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, 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

Paul Horton hopes to bring back WoLF PSORT website at the
same URL, but did not say when.

(I got in touch using his AIST email address, and he replied
from his ISCB email address.)

Peter
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