Hi Bjorn and John,

Thanks for the suggestion regarding the conda dependency resolver. I found
this page:

https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Is there anywhere I can find some examples? I'm unsure how to implement
this feature based on this document.

Thanks!

On Thu, May 5, 2016 at 7:12 AM, John Chilton <jmchil...@gmail.com> wrote:

> Galaxy and Planemo cannot co-exist in the same conda environment I
> don't think - because planemo requires galaxy-lib
> (https://github.com/galaxyproject/galaxy-lib) which cannot be
> installed in Galaxy's environment.
>
> I don't understand the intricacies of what you are trying to do or why
> it worked in the past but not now - there were changes to the way
> planemo creates virtual environments for Galaxy that may interfere
> with this setup but I don't know how to disentangle that. If you can
> figure out exactly what the new planemo is doing wrong (creating a
> virtualenv for Galaxy maybe?) - we can add an option to exclude that
> behavior?
>
> All though -- I'm with Björn - Galaxy can now use installed conda
> environments to resolve requirements for tools. It should be able to
> target and leverage existing conda installations created manually as
> long as the names line up. This was even if you don't use the tool
> shed for installation of tools - you can use the tools in there
> without modification. It may require modifying the conda resolver to
> add the ability to do mapping for your specific setup but this is
> probably something it should do anyway.
>
> -John
>
>
> On Tue, May 3, 2016 at 5:14 PM, Björn Grüning <bjoern.gruen...@gmail.com>
> wrote:
> > Hi,
> >
> > I'm a little bit confused are you using a recent version of Galaxy with
> > conda build-in support and this is not working? Or do you run a Galaxy
> > without conda support and want to set it up?
> >
> > Galaxy can handle conda dependencies for you and tools automatically.
> > Essentially, Galaxy can be configured in galaxy.ini to install it's own
> > miniconda and resolve dependencies on it's own.
> >
> > Hope this helps,
> > Bjoern
> >
> > Am 03.05.2016 um 23:05 schrieb D K:
> >> Hi Galaxy-Devs
> >>
> >> I would like to have a single python / planemo environment that is
> >> portable across computers where I can use planemo test (which
> >> instantiates an instance of Galaxy).
> >>
> >> Currently, we're using conda on our current network. That way we have
> >> shared environments where the version of python and associated modules
> >> is consistent across network computers/users. This way, any user
> >> (including the galaxy system) can use exactly the same python version
> >> and modules which greatly simplifies management. I guess it's possible
> >> to manage dependencies through toolsheds, but we didn't want to do that.
> >>
> >> Although probably not optimal, what we do is to start a conda
> >> environment between the <command> tags in a tool's xml for python
> >> scripts, e.g.:
> >>
> >> <command>
> >> source activate pythonEnv; python Script.py $input1 > $output1
> >> </command>
> >>
> >> The problem is that planemo is also installed in this environment, and
> >> since one cannot start a galaxy instance within a conda environment,
> >> planemo test now fails (since the environment doesn't get loaded
> >> correctly). I can get this to work in planemo 0.14, but not in the newer
> >> versions. Is there a workaround for this, a better setup, or must I stay
> >> with planemo 0.14?
> >>
> >> Thanks!
> >>
> >>
> >>
> >>
> >>
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