Question: IOError: [Errno 13] Permission denied: compiled_templates/grid_base.mako.py
1
gravatar for clijeron
3.2 years ago by
clijeron10
United States
clijeron10 wrote:

Hello everyone,

My name is Carlos and I'm currently working for the City University of New York implementing Galaxy for biomedical research.   I'm new to Galaxy and even Linux world, so please be patient.

After properly installing Galaxy and making the basic changes to the universe_wsgi.ini file, DNS, etc, I found  an error when trying to load data libraries.  I looked around but could not find the same exact problem or solution.  

You can view the exact error message at the following URL:

http://galaxy.hunter.cuny.edu:8080/_debug/view/1410878278

Any ideas on how to resolve this issue ?  Your help will be greatly appreciated.

 

Thank you!
CL

 

galaxy error • 1.9k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by clijeron10

I think John's on the right track here, but I'd also add that running with debug=True should really never be done on a publicly exposed Galaxy server.

ADD REPLYlink written 3.2 years ago by Dannon Baker3.6k

 

 

I had the same problem, and looked into

/mnt/galaxy/database/compiled_templates/library/common/:
total 400K
....

-rw--w--w- 1 galaxy galaxy 2.7K Oct 28 00:13 library_item_info.mako.py
-rw--w--w- 1 galaxy galaxy 2.4K Oct 28 00:13 library_item_info.mako.pyc
-rw-rw-rw- 1 galaxy galaxy 4.3K Oct 22 22:15 library_permissions.mako.py
-rw-rw-rw- 1 galaxy galaxy 4.0K Oct 22 22:15 library_permissions.mako.pyc
-rw--w--w- 1 root   root   4.2K Oct 28 00:30 new_folder.mako.py
-rw--w--w- 1 root   root   4.2K Oct 28 00:30 new_folder.mako.pyc
-rw--w--w- 1 root   root   7.2K Oct 28 00:28 upload.mako.py
-rw--w--w- 1 root   root   5.7K Oct 28 00:28 upload.mako.pyc

All were galaxy owner / group except the last few (which create the erroneous traceback during shared library load). Are they compiled after galaxy boots up for the first time ? I run it as a system service. 

Once I've chown, chgrp these last ones to galaxy user, it works fine.

 

ADD REPLYlink written 3.1 years ago by agbiotec0
1
gravatar for jmchilton
3.2 years ago by
jmchilton1.0k
United States
jmchilton1.0k wrote:

This is very odd - did you modify the permissions of `/home/oem/galaxy-dist/database/` as a super user? What is the output of running the command from the terminal:

ls -lsha /home/oem/galaxy-dist/database/

 

ADD COMMENTlink written 3.2 years ago by jmchilton1.0k
0
gravatar for clijeron
3.2 years ago by
clijeron10
United States
clijeron10 wrote:

Thanks for the feedback John / Dannon !!

After my posting a colleague was able to modify the permissions on the directory in a way that users within the Galaxy system could read the datasets and also the user who starts the Galaxy instance could have read/write access.   So, this worked out well and I'm glad I was able to get some hands on exposure on how to fix this issue.    Thanks again !

 

CL

ADD COMMENTlink written 3.2 years ago by clijeron10

Great, glad you worked it out!

ADD REPLYlink written 3.2 years ago by Dannon Baker3.6k
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