Re: [galaxy-dev] Fwd: Workflow Execution Files

[Aysam Guerler]

Hey Katherine,

Do you attach the values to a valid step? If so I have to look more into it
in order to figure out why the values do not make it through.

Thanks,
Sam

On Mon, Oct 24, 2016 at 2:55 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

>
> -- Forwarded message --
> From: Katherine Beaulieu 
> Date: Mon, Oct 24, 2016 at 2:55 PM
> Subject: Re: [galaxy-dev] Workflow Execution Files
> To: Aysam Guerler 
>
>
> Awesome thanks Aysam! I was wondering if you know what happens to the job
> parameters once they go through 'POST'? I am trying to add my own parameter
> which should show up in the database. I was successful for an individual
> job in tool-form.js, by just adding an attribute to the job_def.inputs
> parameter but in tool-form-composite.js, just adding a parameter to
> job_def.parameters[step size][job_input_id] doesn't automatically add to
> the database.
> Thanks for the help!
>
> On Mon, Oct 24, 2016 at 9:57 AM, Aysam Guerler 
> wrote:
>
>> Hi Katherine,
>>
>> The tool form is build and submitted to the API through
>> tool-form-composite.js.
>>
>> Sam
>>
>> On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu <
>> katherine.beaulieu...@gmail.com> wrote:
>>
>>> Hi Everyone,
>>> Does anyone know what files workflow execution goes through? I had
>>> assumed it just went through the same files as individual jobs for each
>>> step but I don't think that's the case. I was looking at tool-form.js but
>>> it doesn't seem to be executing that file.
>>> Thanks!
>>> Katherine
>>>
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>>
>>
>
>
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Re: [galaxy-dev] 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  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/
>
>
>
>
> ___
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>
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[galaxy-dev] 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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