tool dependencies

classic Classic list List threaded Threaded
2 messages 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.

Cheers,
Matthias








--

-------------------------------------------
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], www.ufz.de

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
Reply | Threaded
Open this post in threaded view
|

Re: tool dependencies

John Chilton-4
On Thu, Nov 16, 2017 at 12:01 PM, Matthias Bernt <[hidden email]> wrote:

> 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)?


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.

>
> Cheers,
> Matthias
>
>
>
>
>
>
>
>
> --
>
> -------------------------------------------
> 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], www.ufz.de
>
> 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:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/