Re: [galaxy-dev] Tmhmm and signal P

2015-11-15 Thread Peter Cock
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, 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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Re: [galaxy-dev] Tmhmm and signal P

2015-11-13 Thread Olivier CLAUDE
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:p.j.a.c...@googlemail.com] 
Envoyé : jeudi 12 novembre 2015 17:35
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

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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Re: [galaxy-dev] Tmhmm and signal P

2015-11-13 Thread Peter Cock
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,
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: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Björn Grüning
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:
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> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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Re: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread 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 
 
mailto:bjoern.gruen...@gmail.com] 
Envoyé : jeudi 12 novembre 2015 12:48
À : Olivier CLAUDE <o.cla...@outlook.fr>
Cc : 'galaxy-dev' <galaxy-...@lists.bx.psu.edu>
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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Re: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Peter Cock
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 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 
>  
> 

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: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread 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=/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 
>  
> 

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: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Peter Cock
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 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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