I'm not worried about it replacing the system python. In general, I am just
trying to learn more about how environments are set for jobs.


On Wed, Jul 27, 2016 at 10:23 PM, Raymond Wan <> wrote:

> Hi Anthony,
> On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner
> <> wrote:
> > I have galaxy server 15.10 running on Ubuntu 14.04, which has python
> 2.7.5.
> >
> > I was in the process of adding matplotlib from the toolchest. It has a
> > dependency on package_python_2_7.
> >
> > Before proceeding, I'd like to understand a bit how that works. Does that
> > install a whole new python, and how then does it get invoked?
> I have a limited understanding of Galaxy compared to Gildas and many
> others here, but it seems that Galaxy and its tools are separated from
> the rest of the system.  So, installing a tool won't affect the system
> unless your users have set a PATH to Galaxy's tool directory.
> For example, when it installs the bwa tool, a bwa executable will get
> installed deep within Galaxy's directories.  But as long as your users
> set their PATH to /usr/bin or /usr/local/bin or wherever you may have
> bwa installed, they'll be fine.  We have this setup where the server
> that runs Galaxy also serves users via ssh.  So far, so good --
> Galaxy's tool installations don't seem to affect the system's packages
> (whether it is something minor like bwa or major like Python).  I'm
> afraid I don't know how it is invoked behind-the-scenes, though.
> The only issue I've encountered so far is the other way.  Software
> installation into the system affects Galaxy.  This was the case with
> Samtools and it happened to me just a couple of months ago.  You can
> take a look at my question and the many helpful replies I got here:
> .  It seems to be the case of just samtools for me (so far).
> I hoe this helps!
> Ray
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