Re: [galaxy-dev] trinity tool form not allowing "None" input for strand-specificity

2015-05-11 Thread Peter Cock 
On Fri, May 8, 2015 at 6:55 PM, Nicola Soranzo  wrote:
> The problem is not in the Cheetah code, which does not get executed because
> of the validation error.
>
> I think this a Galaxy bug which tries to validate the parameter values but
> interprets the value "None" of the library_type param as "no option
> selected".
>
> Nicola

I think this is due to the Python special None object being turned
into the string "None" at some point in the Cheetah template code.

It may be possible to avoid this by a case variant, e.g. "NONE" or
"none", but it may be safer to avoid this special word :(

Peter
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Re: [galaxy-dev] trinity tool form not allowing "None" input for strand-specificity

2015-05-11 Thread Christian Schudoma (TSL) 
Hi Nicola

It happens with both versions available on the main toolshed. We originally had 
the package from bhaas, latest revision from 2012 and yesterday I installed the 
one from biomonika which requires package_trinityrnaseq_2013_08_14 (which in 
turn downloads a copy of trinity).
Both have the same problem.

Since a None value for the strand-spec. parameter means that the parameter is 
ignored (in the Cheetah code) I would think that the issue does not go down to 
the tool level (I can run Trinity on the command line just fine without 
specifying the strand-spec.)

Thanks
Christian

On 08/05/15 17:51, Nicola Soranzo wrote:
Hi Christian,
was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just 
to check this is not a tool problem.

Cheers,
Nicola

Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto:

Hi all,

I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool 
Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as 
"None" will prevent the form from being submitted. Instead, the 
strand-specificity input box will be highlighted in red and I'm asked to 
"Please verify this parameter."

Before the last update we were running a very very old instance of Galaxy (I 
think the update before the last was in 2013) from which we could submit 
trinity-jobs just fine. I found a commit from Aysam from late 2014 which does 
something in the immediate vicinity of the "Please verify this parameter" - 
message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/), 
which I am guessing could have something to do with it.

Anyone got any ideas regarding this? Any help would be appreciated.


Thanks
Christian


--
Dr. Christian Schudoma
Bioinformatics Support Officer

Bioinformatics Group
The Sainsbury Laboratory
Norwich Research Park
Norwich NR4 7UH
United Kingdom
**
+44 (0) 1603 450 601
christian.schud...@tsl.ac.uk
twitter: @cpt_bwt





Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le 
video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
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Re: [galaxy-dev] trinity tool form not allowing "None" input for strand-specificity

2015-05-08 Thread Nicola Soranzo 
  The problem is not in the Cheetah code, which does not get executed
because of the validation error.

I think this a Galaxy bug which tries
to validate the parameter values but interprets the value "None" of the
library_type param as "no option selected".

Nicola

Il 08.05.2015 19:18
Christian Schudoma (TSL) ha scritto: 

> Hi Nicola
> 
> It happens with
both versions available on the main toolshed. We originally had the
package from bhaas, latest revision from 2012 and yesterday I installed
the one from biomonika which requires package_trinityrnaseq_2013_08_14
(which in turn downloads a copy of trinity).
> Both have the same
problem.
> 
> Since a None value for the strand-spec. parameter means
that the parameter is ignored (in the Cheetah code) I would think that
the issue does not go down to the tool level (I can run Trinity on the
command line just fine without specifying the strand-spec.)
> 
>
Thanks
> Christian
> 
> On 08/05/15 17:51, Nicola Soranzo wrote: 
> 
>>
Hi Christian,
>> was the trinityrnaseq tool installed from the Tool
Shed? Which repository? Just to check this is not a tool problem.
>> 
>>
Cheers,
>> Nicola
>> 
>> Il 08.05.2015 10:44 Christian Schudoma (TSL) ha
scritto: 
>> 
>>> Hi all,
>>> 
>>> I have encountered a problem when
trying to run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy.
Leaving the strand-specificity input parameter as "None" will prevent
the form from being submitted. Instead, the strand-specificity input box
will be highlighted in red and I'm asked to "Please verify this
parameter."
>>> 
>>> Before the last update we were running a very very
old instance of Galaxy (I think the update before the last was in 2013)
from which we could submit trinity-jobs just fine. I found a commit from
Aysam from late 2014 which does something in the immediate vicinity of
the "Please verify this parameter" - message.
(https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/ [1]),
which I am guessing could have something to do with it.
>>> 
>>> Anyone
got any ideas regarding this? Any help would be appreciated.
>>> 
>>>
Thanks
>>> Christian
>>> 
>>> --
>>> Dr. Christian Schudoma
>>>
Bioinformatics Support Officer
>>> 
>>> Bioinformatics Group
>>> The
Sainsbury Laboratory
>>> Norwich Research Park
>>> Norwich NR4 7UH
>>>
United Kingdom
>>> **
>>> +44 (0) 1603 450
601
>>> christian.schud...@tsl.ac.uk [2]
>>> twitter: @cpt_bwt
>> 
>>
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
le video chiamate e persino le chiamate di gruppo.
>> E chiami gratis
anche i numeri fissi e mobili nel mondo!
>> Scarica subito l'app Vai su
https://www.indoona.com/ [3]
  


Connetti gratis il mondo con la nuova indoona:  hai la chat, le chiamate, le 
video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/

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Re: [galaxy-dev] trinity tool form not allowing "None" input for strand-specificity

2015-05-08 Thread Nicola Soranzo 
  Hi Christian,
was the trinityrnaseq tool installed from the Tool
Shed? Which repository? Just to check this is not a tool
problem.

Cheers,
Nicola

Il 08.05.2015 10:44 Christian Schudoma (TSL)
ha scritto: 

> Hi all,
> 
> I have encountered a problem when trying to
run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy. Leaving the
strand-specificity input parameter as "None" will prevent the form from
being submitted. Instead, the strand-specificity input box will be
highlighted in red and I'm asked to "Please verify this parameter."
> 
>
Before the last update we were running a very very old instance of
Galaxy (I think the update before the last was in 2013) from which we
could submit trinity-jobs just fine. I found a commit from Aysam from
late 2014 which does something in the immediate vicinity of the "Please
verify this parameter" - message.
(https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/ [1]),
which I am guessing could have something to do with it.
> 
> Anyone got
any ideas regarding this? Any help would be appreciated.
> 
> Thanks
>
Christian
> 
> --
> Dr. Christian Schudoma
> Bioinformatics Support
Officer
> 
> Bioinformatics Group
> The Sainsbury Laboratory
> Norwich
Research Park
> Norwich NR4 7UH
> United Kingdom
>
**
> +44 (0) 1603 450 601
>
christian.schud...@tsl.ac.uk [2]
> twitter: @cpt_bwt
 



Connetti gratis il mondo con la nuova indoona:  hai la chat, le chiamate, le 
video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/

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[galaxy-dev] trinity tool form not allowing "None" input for strand-specificity

2015-05-08 Thread Christian Schudoma (TSL) 
Hi all,

I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool 
Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as 
"None" will prevent the form from being submitted. Instead, the 
strand-specificity input box will be highlighted in red and I'm asked to 
"Please verify this parameter."

Before the last update we were running a very very old instance of Galaxy (I 
think the update before the last was in 2013) from which we could submit 
trinity-jobs just fine. I found a commit from Aysam from late 2014 which does 
something in the immediate vicinity of the "Please verify this parameter" - 
message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/), 
which I am guessing could have something to do with it.

Anyone got any ideas regarding this? Any help would be appreciated.


Thanks
Christian


--
Dr. Christian Schudoma
Bioinformatics Support Officer

Bioinformatics Group
The Sainsbury Laboratory
Norwich Research Park
Norwich NR4 7UH
United Kingdom
**
+44 (0) 1603 450 601
christian.schud...@tsl.ac.uk
twitter: @cpt_bwt


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