Are you trying to install this?

https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e9637...

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 jochen.bick@usys.ethz.ch 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

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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/05977e9637...

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 jochen.bick@usys.ethz.ch 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/05977e9637...

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 jochen.bick@usys.ethz.ch 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

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-- 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 jochen.bick@usys.ethz.ch mailto:jochen.bick@usys.ethz.ch 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/

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On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick jochen.bick@usys.ethz.ch 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