Hey Fernandez,

The proxy configuration can be tricky to configure when setting up external display applications, xsendfile (https://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy), etc.... The problem is that Apache and Galaxy need to access all of the same files and directories. I suspect many institutions have deployed Galaxies in this manner. In my previous position at MSI we found everything was much easier to configure when we ran our Apache process as the same user as Galaxy - I would really recommend this if possible - it makes reasoning about file and directory permissions much more straight forward.

In response to your second question about the functional tests - that last error occurs a lot but is not that interesting - it just is some problem cleaning up some directory or file as the Galaxy web server instance the test suite starts up shuts down - it is not indicating a test failure or anything. Your test instance seemed to load a lot of tools so you should have had more tools running tests - do not know why none ran. I will continue to think about what can cause this... I really have no clue.

If you are really interested in getting these tests to run - can you send me the output of these commands:

./run_functional_tests.sh -list ./run_functional_tests.sh -id cat1

-John

On Thu, Dec 19, 2013 at 12:55 PM, Fernandez Edgar edgar.fernandez@umontreal.ca wrote:

Hello everyone,

So I’ve successfully installed on rhel6 a production environment of galaxy with an apache proxy.

Unavoidably, I have some question when it comes to the permissions of the galaxy directory :

Currently, all the galaxy directory is

a. chown –R galaxy: users /home/galaxy/galaxy-dist

b. chmod –R 700 /home/galaxy/galaxy-dist

Will this cause me some issues with the apache proxy?

Furthermore, I’ve try to run run_functional_tests.sh and I get a log file that you can find in attachment.

Can you please explain the last error and why don’t I get any successful tests?

Lastly, I was wondering if it’s possible to move the directory /home/galaxy/galaxy-dist/database somewhere else,

and create a logical link instead (/home/galaxy/galaxy-dist/database --> /another/path/database)?

Cordialement / Regards,

Edgar Fernandez

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