I forgot to say that Galaxy installs those dependencies (tool_dependencies or conda) beside your host system. That will not interfere with your host libraries, binaries ... Gildas ----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/> Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------

Le 27 juil. 2016 à 17:41, Gildas Le Corguillé <lecorguille@sb-roscoff.fr> a écrit :

Hi Tony,

Yes, Galaxy will install a whole functional python version. At runtime, Galaxy source some env.sh files according to the different requirements and the bunch of requirement dependencies.

Using the tool_dependencies, indeed, Galaxy sets almost a dedicated environment for the tools.

The purpose is the same with the new system Conda. But in this case, Conda can create environment natively

I hope I answered to your question.

Gildas

----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science) http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 ------------------------------------------------------------------

...

Le 27 juil. 2016 à 17:16, Tony Schreiner <anthony.schreiner@bc.edu <mailto:anthony.schreiner@bc.edu>> a écrit :

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?

Tony Schreiner ___________________________________________________________ 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: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>

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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. Tony On Wed, Jul 27, 2016 at 10:23 PM, Raymond Wan <rwan.work@gmail.com> wrote:

Hi Anthony,

On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner <anthony.schreiner@bc.edu> 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:

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!

Ray