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?

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:

To search Galaxy mailing lists use the unified search at:

Reply via email to