diff options
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 32 |
1 files changed, 32 insertions, 0 deletions
@@ -19,6 +19,38 @@ deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers). See the [installation docs](doc/README.org). +## Configuration + +GeneNetwork2 comes with a [default configuration file](./etc/default_settings.py) +which can be used as a starting point. + +The recommended way to deal with the configurations is to **copy** this default configuration file to a location outside of the repository, say, + +```sh +.../genenetwork2$ cp etc/default_settings.py "${HOME}/configurations/gn2.py" +``` + +then change the appropriate values in the new file. You can then pass in the new +file as the configuration file when launching the application, + +```sh +.../genenetwork2$ bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run> +``` + +The other option is to override the configurations in `etc/default_settings.py` +by setting the configuration you want to override as an environment variable e.g. +to override the `SQL_URI` value, you could do something like: + +```sh +.../genenetwork2$ env SQL_URI="mysql://<user>:<passwd>@<host>:<port>/<db_name>" \ + bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run> +``` + +replacing the placeholders in the angle brackets with appropriate values. + +For a detailed breakdown of the configuration variables and their use, see the +[configuration documentation](doc/configurations.org) + ## Run Once having installed GN2 it can be run through a browser |