trinity tool form not allowing "None" input for strand-specificity

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trinity tool form not allowing "None" input for strand-specificity

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
[hidden email]
twitter: @cpt_bwt



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Re: trinity tool form not allowing "None" input for strand-specificity

Nicola Soranzo-2
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
[hidden email]
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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Re: trinity tool form not allowing "None" input for strand-specificity

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
[hidden email]
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/



___________________________________________________________
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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Re: trinity tool form not allowing "None" input for strand-specificity

Nicola Soranzo-2
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/), 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
[hidden email]
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/




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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in your mail client.  To manage your subscriptions to this
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Re: trinity tool form not allowing "None" input for strand-specificity

Peter Cock
On Fri, May 8, 2015 at 6:55 PM, Nicola Soranzo <[hidden email]> 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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