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,
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.:
> source activate pythonEnv; python Script.py $input1 > $output1
> 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?
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