Ballgown does not work
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
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
___________________________________________________________ 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/
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
___________________________________________________________ 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 jochen.bick@usys.ethz.ch <mailto:jochen.bick@usys.ethz.ch> www.ap.ethz.ch
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
___________________________________________________________ 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 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
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/05977e9637...
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.
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($dataset.element_identifier) #end if #end def Cheers Jochen
On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick <jochen.bick@usys.ethz.ch> wrote:
Hi Peter,
I can contact report the issue on github.
I think that would be best.
It looks like its looking for a variable called dataset with is not defined in the input part.
this looks like python code?:
##------------------------------------------------------------------------------------ ## This function returns the name of the sample associated to a given file ##------------------------------------------------------------------------------------ #def get_sample_name($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
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/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
___________________________________________________________ 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/
participants (3)
-
Jochen Bick -
Nicola Soranzo -
Peter Cock