tool dependencies

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tool dependencies

Matthias Bernt
Hi all,

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.

Cheers,
Matthias








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-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
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