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.
Check out your configuration at
config/galaxy.ymland look for non-galaxy-folder paths, maybe something liketool_dependency_dirin https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L217Only 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.