On Thu, Nov 16, 2017 at 12:01 PM, Matthias Bernt firstname.lastname@example.org wrote:
I tried to install velvetoptimizer (for the assembly tutorial in the GTN).
It lists velvetoptimiser as requirement in the main xml and the tool_dependencies.xml (listing the installation steps). Now there seems to be a conda package perl-velvetoptimiser.
What would be the steps to to update the tool (I would happily create a PR)? Is the tool_dependencies.xml intended to be kept and I just need to update the names of the requirements (I guess the name in the tool_dependencies.xml does not matter)?
I'd open a PR to adjust the requirement names to match the Conda package and drop the tool_dependencies.xml all together.
Furthermore the tool_dependencies.xml includes the package_velvet which is listed as missing dependency in the management pages. Shouldn't this be ignored if there is a conda package?
For reproducibility reasons by default Galaxy will prefer a tool_dependencies.xml file over Conda packages, this is why it is best just to drop the tool_dependencies.xml file all together if possible.
Last question: Is it possible to update an installed package by editing the xml files? It seemed to me that changes do not have an effect.
For tool shed packages? I don't think so. This probably works for tools but the packages have already been installed.
Hope this helps and sorry for the delay.
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, email@example.com, www.ufz.de
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