Victor;
I noticed some chances in the repository which give the following error. sudo python scripts/nglims/add_ng_defaults.py universe_wsgi.ini
This doesn't affect your problem, but you don't need to run this script as root.
Traceback (most recent call last): IOError: [Errno 2] No such file or directory: '/opt/glims/galaxy-central/lib/galaxy/util/../../../tool-data/shared/ucsc/builds.txt' [...] I also see the error below when trying to start galaxy. galaxy-central > ./run.sh Traceback (most recent call last): ConfigurationError: Directory does not exist: ./database/files
Have you run the setup script ('sh setup.sh') on this repository? Both the files you are missing will be created by it. You'll want to run setup.sh and run.sh at least once on a brand new repository before running the nglims script: http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims Hope this helps, Brad