tool dependencies

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

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.



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,
[hidden email],

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at: