Ballgown does not work

classic Classic list List threaded Threaded
7 messages Options
| Threaded
Open this post in threaded view
|

Ballgown does not work

Jochen
Hi,

I'm trying to install Ballgown but it throws some error message after
running it:

cannot find 'dataset' while searching for 'param_name.dataset.dataset'

the script does not have test-data file and it also does not install the
requirements.

Cheers Jochen

___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Peter Cock
Are you trying to install this?

https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b

If so, it does set out its requirements:

    <requirements>
        <requirement type="package"
version="2.2.0">bioconductor-ballgown</requirement>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
        <requirement type="package" version="1.3.2">r-optparse</requirement>
    </requirements>

However, your Galaxy would have to be using BioConda to do this.
This wrapper does not include a legacy Galaxy XML file to declare
its package dependencies.

What version of Galaxy do you have?

Peter

On Tue, Apr 10, 2018 at 2:16 PM, Jochen Bick <[hidden email]> wrote:

> Hi,
>
> I'm trying to install Ballgown but it throws some error message after
> running it:
>
> cannot find 'dataset' while searching for 'param_name.dataset.dataset'
>
> the script does not have test-data file and it also does not install the
> requirements.
>
> Cheers Jochen
>
> ___________________________________________________________
> 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/
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Jochen
Hej Peter,

thanks for the quick reply. My galaxy is a release_17.05

I think the xml is also broken.

Cheers Jochen

On 10.04.2018 15:28, Peter Cock wrote:

> Are you trying to install this?
>
> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
>
> If so, it does set out its requirements:
>
>     <requirements>
>         <requirement type="package"
> version="2.2.0">bioconductor-ballgown</requirement>
>         <requirement type="package" version="0.5.0">r-dplyr</requirement>
>         <requirement type="package" version="1.3.2">r-optparse</requirement>
>     </requirements>
>
> However, your Galaxy would have to be using BioConda to do this.
> This wrapper does not include a legacy Galaxy XML file to declare
> its package dependencies.
>
> What version of Galaxy do you have?
>
> Peter
>
> On Tue, Apr 10, 2018 at 2:16 PM, Jochen Bick <[hidden email]> wrote:
>> Hi,
>>
>> I'm trying to install Ballgown but it throws some error message after
>> running it:
>>
>> cannot find 'dataset' while searching for 'param_name.dataset.dataset'
>>
>> the script does not have test-data file and it also does not install the
>> requirements.
>>
>> Cheers Jochen
>>
>> ___________________________________________________________
>> 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/

--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
Office: Tannenstrasse 1 / TAN D 6.2
8092 Zurich, Switzerland

Phone +41 44 632 28 25
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Peter Cock
Hi Jochen,

If you are using release_17.05, that should be using (bio)conda
for dependencies:

https://docs.galaxyproject.org/en/latest/admin/conda_faq.html

"The short answer is that as of 17.01, Galaxy should install Conda
the first time it starts up and be configured to use it by default."

The Galaxy administration screen should let you review if you
have got ballgown itself installed like this, or not.

You didn't confirm which Ballgown you were trying to use in
Galaxy. Is it this version from Theo Collard:

https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b

If so, this appears to be where he develops it on GitHub, you
could file an issue there:

https://github.com/CollardT/Ballgown-Wrapper

Peter

On Tue, Apr 10, 2018 at 2:37 PM, Jochen Bick <[hidden email]> wrote:

> Hej Peter,
>
> thanks for the quick reply. My galaxy is a release_17.05
>
> I think the xml is also broken.
>
> Cheers Jochen
>
> On 10.04.2018 15:28, Peter Cock wrote:
>> Are you trying to install this?
>>
>> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
>>
>> If so, it does set out its requirements:
>>
>>     <requirements>
>>         <requirement type="package"
>> version="2.2.0">bioconductor-ballgown</requirement>
>>         <requirement type="package" version="0.5.0">r-dplyr</requirement>
>>         <requirement type="package" version="1.3.2">r-optparse</requirement>
>>     </requirements>
>>
>> However, your Galaxy would have to be using BioConda to do this.
>> This wrapper does not include a legacy Galaxy XML file to declare
>> its package dependencies.
>>
>> What version of Galaxy do you have?
>>
>> Peter
>>
>> On Tue, Apr 10, 2018 at 2:16 PM, Jochen Bick <[hidden email]> wrote:
>>> Hi,
>>>
>>> I'm trying to install Ballgown but it throws some error message after
>>> running it:
>>>
>>> cannot find 'dataset' while searching for 'param_name.dataset.dataset'
>>>
>>> the script does not have test-data file and it also does not install the
>>> requirements.
>>>
>>> Cheers Jochen
>>>
>>> ___________________________________________________________
>>> 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/
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> Office: Tannenstrasse 1 / TAN D 6.2
> 8092 Zurich, Switzerland
>
> Phone +41 44 632 28 25
> [hidden email] <mailto:[hidden email]>
> www.ap.ethz.ch
> ___________________________________________________________
> 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/
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Jochen
Hi Peter,


> "The short answer is that as of 17.01, Galaxy should install Conda
> the first time it starts up and be configured to use it by default."

yes, it installs everything with conda. So that should work, but I could
also set it up my self manually.


> You didn't confirm which Ballgown you were trying to use in
> Galaxy. Is it this version from Theo Collard:
>
> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
>
> If so, this appears to be where he develops it on GitHub, you
> could file an issue there:

and yes that is the version I'm trying to install.

>
> https://github.com/CollardT/Ballgown-Wrapper

I can contact report the issue on github. It looks like its looking for
a variable called dataset with is not defined in the input part.

this looks like python code?:

##------------------------------------------------------------------------------------
## This function returns the name of the sample associated to a given file
##------------------------------------------------------------------------------------
#def get_sample_name($dataset, $sample_mapping):
    ##If the file with samples mapping was provided
    #if $sample_mapping != None:
        #return $sample_mapping.get($dataset.name, None)
    ##Otherwise with extract the sample name from the filename
    #else:
        #return str($dataset.element_identifier)
    #end if
#end def

Cheers Jochen
___________________________________________________________
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/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Peter Cock
On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick <[hidden email]> wrote:
> Hi Peter,
>
>
>>
>> https://github.com/CollardT/Ballgown-Wrapper
>
> I can contact report the issue on github.

I think that would be best.

> It looks like its looking for
> a variable called dataset with is not defined in the input part.
>
> this looks like python code?:
>
> ##------------------------------------------------------------------------------------
> ## This function returns the name of the sample associated to a given file
> ##------------------------------------------------------------------------------------
> #def get_sample_name($dataset, $sample_mapping):
>     ##If the file with samples mapping was provided
>     #if $sample_mapping != None:
>         #return $sample_mapping.get($dataset.name, None)
>     ##Otherwise with extract the sample name from the filename
>     #else:
>         #return str($dataset.element_identifier)
>     #end if
> #end def
>
> Cheers Jochen

Sort of. It is a templating language called Cheetah which
supports of lot of Python syntax:

http://cheetahtemplate.org/

Most Galaxy wrappers at most use this for if-statements and
for-loops, this might be the first time I've seen complicated
functions being defined in Cheetah code like this.

It would help greatly if the tool author provided a test dataset
(and even better used this to define a tool self-test).

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:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Ballgown does not work

Nicola Soranzo-2
In reply to this post by Jochen
Hi Jochen,
Theo also opened a pull request to submit it to IUC:

https://github.com/galaxyproject/tools-iuc/pull/1366

but hasn't updated it after August 2017.

Cheers,
Nicola

On 10/04/18 14:37, Jochen Bick wrote:

> Hej Peter,
>
> thanks for the quick reply. My galaxy is a release_17.05
>
> I think the xml is also broken.
>
> Cheers Jochen
>
> On 10.04.2018 15:28, Peter Cock wrote:
>> Are you trying to install this?
>>
>> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
>>
>> If so, it does set out its requirements:
>>
>>      <requirements>
>>          <requirement type="package"
>> version="2.2.0">bioconductor-ballgown</requirement>
>>          <requirement type="package" version="0.5.0">r-dplyr</requirement>
>>          <requirement type="package" version="1.3.2">r-optparse</requirement>
>>      </requirements>
>>
>> However, your Galaxy would have to be using BioConda to do this.
>> This wrapper does not include a legacy Galaxy XML file to declare
>> its package dependencies.
>>
>> What version of Galaxy do you have?
>>
>> Peter
>>
>> On Tue, Apr 10, 2018 at 2:16 PM, Jochen Bick <[hidden email]> wrote:
>>> Hi,
>>>
>>> I'm trying to install Ballgown but it throws some error message after
>>> running it:
>>>
>>> cannot find 'dataset' while searching for 'param_name.dataset.dataset'
>>>
>>> the script does not have test-data file and it also does not install the
>>> requirements.
>>>
>>> Cheers Jochen
>>>
>>> ___________________________________________________________
>>> 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/

___________________________________________________________
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/