Re: [galaxy-dev] dataset collection datatype

[Björn Grüning]

Hi Cristel,

can you share some code. If you use discover_datasets like this,
format="" should indeed work.



Another feature is that the filetype is extracted from the extension if
you use it like this:

https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/split_file_on_column/split_file_on_column.xml

Ciao,
Bjoern

> Hello galaxy developers,
> 
> how do you set the format for datasets in output dataset collections? I
> looked at some xmls from John Chilton, and tried using
> format_source="input", or inherit_format="true". Those unfortunately do
> not work. I also naively tried format="txt" to no avail.
> 
> I can't find anything in the documentation.
> Can someone point me in the right direction?
> 
> Thanks much,
> Cris
> 
> 
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[galaxy-dev] dataset collection datatype

[Cristel Thomas]

Hello galaxy developers,

how do you set the format for datasets in output dataset collections? I
looked at some xmls from John Chilton, and tried using
format_source="input", or inherit_format="true". Those unfortunately do not
work. I also naively tried format="txt" to no avail.

I can't find anything in the documentation.
Can someone point me in the right direction?

Thanks much,
Cris
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Re: [galaxy-dev] Galaxy in Docker and nginx

[Björn Grüning]

Hi Miuki,

are you referring to this project?

https://github.com/bgruening/docker-galaxy-stable

If so you don't need to take care of anything, this one should be
production ready. If not copy what ever you need :)

Ciao,
Bjoern

Am 28.07.2016 um 22:28 schrieb Yip, Miu ki:
> Hi Galaxy Team,
> 
> I'm currently trying to use Galaxy in Docker, and I wanted to know if
> there are special actions that I have to do in Galaxy for nginx. I'm
> trying to set up a reserve proxy and have url forwarding. Do I need
> to inform Galaxy in Docker that nginx is being use?
> 
> Thanks, Miuki 
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[galaxy-dev] August Galaxy News

[Dave Clements]

Hello all,

The *August Galaxy News
 is out!*

   -

   GCC2016 presentations and training are online
   

   -

   Galaxy Admin Training
   

   -

   Other Upcoming Events
   
   -

   New F1000Research Galaxy Channel
   

   -

   55 new Papers
   
   -

   Open positions
   
(hurry!)
   -

   Public Galaxy Server News
   

   -

   New community hub entries
   
   -

   TooShed Contributions
   
   -

   And other news
    too.

Dave Clements and the Galaxy Team


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] Galaxy in Docker and nginx

[Yip, Miu ki]

Hi Galaxy Team,

I'm currently trying to use Galaxy in Docker, and I wanted to know if there are 
special actions that I have to do in Galaxy for nginx. I'm trying to set up a 
reserve proxy and have url forwarding. Do I need to inform Galaxy in Docker 
that nginx is being use?

Thanks,
Miuki
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[galaxy-dev] Recommended Hardware for Galaxy

[Durdevic, Marija]

Dear all,

In our Center for Medical Research we installed Galaxy server for our 
researchers. We are running Galaxy on login node (Virtual Machine) and job 
execution is on cluster configured using SLURM.
In Galaxy configuration we are using Supervisor-uWSGI-Nginx and two handlers. 
We are facing low performance problem and very slow Galaxy response.

Our Virtual Machine has 4 cores and 16GB of RAM memory. Is there any 
recommended hardware configuration for Galaxy?

Thanks in advance,

Marija

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Re: [galaxy-dev] Storing data in the user session

[Mohamed Kassam]

Dear Bjoern,
I think it should work for me.

I will contatct you to see how it can work for my purpose.

Thank you in advance,

Mohamed

2016-07-28 20:59 GMT+02:00 Björn Grüning :

> Hi Steve & Mohammed,
>
> I'm working on a user-profile extension to get credentials for a user,
> but this will take a few more weeks sorry.
>
> In the meantime can you look at the following idea:
>
> my_programm.py --credentials $USER_CREDENTIALS --arguments
>
> The variable $USER_CREDENTIALS is set during job execution with dynamic
> destination mappings
>
> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping
>
> What do you think, would this work for you?
> This assumes you as admin can pass along the user credentials if you
> know the username.
>
> If not please get in touch and I will tell you about my plans to extend
> the user-preferences maybe you can help me with this to speed things up.
>
> Ciao,
> Bjoern
>
>
> > Hi Bjorn,
> >  sure, I don’t want to have the credentials stored in the tool but the
> tool
> > needs to act on behalf of the user to retrieve data from the repository,
> so
> > it needs access to credentials.  This could for example be a token
> generated
> > via an OAuth2 exchange - basically something that is sent along with
> every
> > http request to the remote resource to authenticate the user.
> >
> > My thought is that this could be stored in the user profile if this can
> be made
> > available to the tool in the same way that __user_email__ is now.
> >
> > When you say ‘on the framework level’ do you mean by Galaxy?
> >
> > Steve
> > —
> > Department of Computing, Macquarie University
> > http://web.science.mq.edu.au/~cassidy
> >
> >> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> wrote:
> >>
> >> Hi Steve,
> >>
> >> can you explain the larger use-case behind it. Imho you should not
> >> populate a tool with credentials, this should be handled on the
> >> framework level.
> >>
> >> Hope you are fine,
> >> Bjoern
> >>
> >> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> >>> Hi again,
> >>>   I’m looking for the right way to store some user credentials in the
> >>> galaxy session so that tools can work on behalf of the user with our
> >>> repository.
> >>>
> >>> Currently users have an API key and they need to upload it as a data
> >>> item to that is then passed to each tool that needs it as input.  This
> >>> doesn’t seem like the right solution since the API key becomes part of
> >>> the history and so would be shared if the history were shared.
> >>>
> >>> What would be better would be a way of storing the API key in the user
> >>> session and then being able to pass that into a tool.
> >>>
> >>> I note that there are a few user session variables available in the
> tool
> >>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> >>> There is also a user preferences page where they can fill out a few
> >>> details.  However, I can’t see a mechanism to extend this in any way
> and
> >>> have extra properties in the preferences pane that would then be
> >>> available to tools via the template file.
> >>>
> >>> I can see that the standard practice for the data sources on
> >>> usegalaxy.org  is to send the user off to a
> >>> repository website to find data that is then posted back to the galaxy
> >>> server.  This isn’t appropriate for us since the interaction with the
> >>> repository is not just for downloading a single dataset - tools will
> >>> query the repository, download various kinds of data and possibly
> upload
> >>> new data, so we need to store user credentials in some way.
> >>>
> >>> Is there already a good way to achieve this or is this an enhancement
> to
> >>> Galaxy?
> >>>
> >>> Thanks,
> >>>
> >>> Steve
> >>>
> >>>
> >>> —
> >>> Department of Computing, Macquarie University
> >>> http://web.science.mq.edu.au/~cassidy
> >>> 
> >>>
> >>>
> >>>
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>
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