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
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