Re: [galaxy-dev] multiple datatypes input in 16.07

[Cristel Thomas]

Hey Sam,
thanks, I'll check tomorrow at work but I suspect there might be something
else - I use rpy2 to call R, so that FCS files can be read. As of 2 months
ago there was no efficient way of doing it strictly in python. rpy2 does
not load if R isn't installed on the system (and for this specific script,
it requires flowCore installed in R).
We have R installed on our instance and still have the issues I described
earlier (though I will double check tomorrow and keep you posted).

In the long run the rpy2 thing might be an issue. We want to add our tools
and the datatypes to galaxy. I'm not sure how to get around to doing it
without rpy2. I'd like to keep a sniffer function in there.

Thanks again,
Cris

On Tue, Dec 13, 2016 at 1:24 PM, Aysam Guerler 
wrote:

> Hey Cris,
>
> Dannon and I figured out, that the problem is that your datatypes are not
> loaded properly, due to these two invalid imports:
>
> https://github.com/ImmPortDB/immport-galaxy/blob/release_
> 16.07/lib/galaxy/datatypes/flow.py#L13
>
> Removing them fixes the issue. The error for this is shown in the server
> log.
>
> Thanks,
> Sam
>
___
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/

[galaxy-dev] Testing workflows

[Eric Rasche]

Wondering if anyone has tooling to test a workflow as it exists in a
specific galaxy instance? I'm looking to test some of my user's manually
built workflows in our galaxy instance to make sure that we can detect
issues when they arise (e.g. due to changes in the interfaces of our
non-toolshed installed tools)

Ideally something like:

$ my_tool $galaxy_url $api_key $workflow_id
  
> report.xunit.xml

If not we'll build something soon.

Cheers,
Eric
___
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/