Question: Server only works properly when launched as root, not as galaxy user.
0
gravatar for mdgronke
9 weeks ago by
mdgronke10
mdgronke10 wrote:

I have a problem where I cannot install or update tools if I launch the server as user galaxy.

Here is what I have tried:

-Chowning the entire galaxy directory, including all hidden folders, to be owned by galaxy. I've confirmed this has been done. But after launching the server as user galaxy, I cannot install or update tools.

-If I execute the run.sh as root, the server runs and I am now able to install/update tools. This does end up changing the integrated_tool_panel.xml to be owned by root.

I am basically 99.9% sure this means a permission issue SOMEWHERE, but at this point I am at a loss. All of the galaxy folders were chowned to galaxy. So what remains? Are there some other folders out there on my server, somewhere, that need to be owned to galaxy for this to work?

Or is it possible the galaxy user does not have proper write permissions? How can I verify this?

edit:

Here is updated knowledge:

I have tried the following:

a. Running /galaxy/.venv/bin/uwsgi --yaml /galaxy/config/galaxy.yml will host the server, but will not allow me to install tools.

b. Running sudo /galaxy/.venv/bin/uwsgi --yaml /galaxy/config/galaxy.yml will host the server, but will not allow me to install tools.

c. Running ./run.sh will host the server, but not allow me to install tools.

d. Running sudo ./run.sh will host the server, and allow me to install tools.

uwsgi config permissions server • 152 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by mdgronke10

Check out your configuration at config/galaxy.yml and look for non-galaxy-folder paths, maybe something like tool_dependency_dir in https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L217

ADD REPLYlink written 9 weeks ago by Martin Čech ♦♦ 4.9k

Only paths listed are .venv for virtual env, and lib for python, both in the same directory and both owned to galaxy.

My tool dependency directory is left to default, so it exists within the galaxy folder as well.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by mdgronke10
0
gravatar for mdgronke
9 weeks ago by
mdgronke10
mdgronke10 wrote:

UPDATE: I have 'solved' the issue. Here is my fix.

My shed-tool folders were set in the apps/ directory, one directory up and alongside galaxy/. These were not chowned to galaxy. I chowned them to galaxy. Then I reran my systemd service (which executes by root but for user galaxy) and it was able to work.

ADD COMMENTlink written 9 weeks ago by mdgronke10
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