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!