Thanks 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 email@example.com wrote:
On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner firstname.lastname@example.org wrote:
I have galaxy server 15.10 running on Ubuntu 14.04, which has python
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:
http://dev.list.galaxyproject.org/Unsorted-BAM-file-gt-Galaxy-crash-td466945... . It seems to be the case of just samtools for me (so far).
I hoe this helps!