On Thu, Nov 16, 2017 at 12:01 PM, Matthias Bernt <m.bernt(a)ufz.de> 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.
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
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