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)?
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?
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.