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odose

Vos, Michiel

 

Dear Galaxy developers,

 

We hereby want to ask if anyone is interested in helping out to repair and update our Galaxy tool ‘odose’:

 

Webserver

 

Publication

 

Public server page

 

Github

 

Odose enables users to perform an array of population genetics tests on prokaryote genomes. Our tool is currently linked to NCBI to download various files, but continuous restructuring at NCBI has resulted in broken links which prevent the pipeline from working. Developer Tim te Beek has moved on outside academia and does not have the time to fix it, but is available to give answer question/give instructions. We believe our tool is highly useful for microbiologists and would greatly appreciate any help from the Galaxy community to get it working properly again! Please get in touch if you would like to know more.

 

Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek

 

 

 

Michiel Vos

European Centre for Environment and Human Health

University of Exeter

ESI Building, Penryn Campus

TR10 9FE Penryn, UK

0044 (0)1326259464

https://coastalpathogens.wordpress.com/

 


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Re: odose

Peter Cock
You might find this work useful for fetching bacteria from the NCBI:

https://github.com/kblin/ncbi-genome-download

Peter

On Tue, Oct 25, 2016 at 12:54 PM, Vos, Michiel <[hidden email]> wrote:

>
>
> Dear Galaxy developers,
>
>
>
> We hereby want to ask if anyone is interested in helping out to repair and
> update our Galaxy tool ‘odose’:
>
>
>
> Webserver
>
>
>
> Publication
>
>
>
> Public server page
>
>
>
> Github
>
>
>
> Odose enables users to perform an array of population genetics tests on
> prokaryote genomes. Our tool is currently linked to NCBI to download various
> files, but continuous restructuring at NCBI has resulted in broken links
> which prevent the pipeline from working. Developer Tim te Beek has moved on
> outside academia and does not have the time to fix it, but is available to
> give answer question/give instructions. We believe our tool is highly useful
> for microbiologists and would greatly appreciate any help from the Galaxy
> community to get it working properly again! Please get in touch if you would
> like to know more.
>
>
>
> Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek
>
>
>
>
>
>
>
> Michiel Vos
>
> European Centre for Environment and Human Health
>
> University of Exeter
>
> ESI Building, Penryn Campus
>
> TR10 9FE Penryn, UK
>
> 0044 (0)1326259464
>
> https://coastalpathogens.wordpress.com/
>
>
>
>
> ___________________________________________________________
> 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/mailinglists/
___________________________________________________________
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/mailinglists/
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Re: odose

Björn Grüning-3
In reply to this post by Vos, Michiel
Hi Michiel,

the IUC (https://github.com/galaxyproject/tools-iuc) is adopting
wrappers and helping with fixing them. Can you create a PR with
everything what you have against this repo, we will review it and guide
you through the process. Once, this is merged we will help maintaining it.

Thanks,
Bjoern

Am 25.10.2016 um 13:54 schrieb Vos, Michiel:

>  
>
> Dear Galaxy developers,
>
>  
>
> We hereby want to ask if anyone is interested in helping out to repair
> and update our Galaxy tool ‘odose’:
>
>  
>
> Webserver <http://www.odose.nl/>
>
>  
>
> Publication
> <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062447>
>
>  
>
> Public server page
> <https://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE>
>
>  
>
> Github <https://github.com/ODoSE/galaxy>
>
>  
>
> Odose enables users to perform an array of population genetics tests on
> prokaryote genomes. Our tool is currently linked to NCBI to download
> various files, but continuous restructuring at NCBI has resulted in
> broken links which prevent the pipeline from working. Developer Tim te
> Beek has moved on outside academia and does not have the time to fix it,
> but is available to give answer question/give instructions. We believe
> our tool is highly useful for microbiologists and would greatly
> appreciate any help from the Galaxy community to get it working properly
> again! Please get in touch if you would like to know more.
>
>  
>
> Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek
>
>  
>
>  
>
>  
>
> Michiel Vos
>
> European Centre for Environment and Human Health
>
> University of Exeter
>
> ESI Building, Penryn Campus
>
> TR10 9FE Penryn, UK
>
> 0044 (0)1326259464
>
> https://coastalpathogens.wordpress.com/
>
>  
>
>
>
> ___________________________________________________________
> 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/mailinglists/
>
___________________________________________________________
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/mailinglists/
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