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Installation

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Joe Futrelle edited this page Aug 10, 2015 · 8 revisions

Follow the instructions for your operating system:

Configuration

The command-line interface requires that you, or someone in your lab, has completed the Database Installation. Once that step is done you will be able to configure the CLI to connect to your database.

To connect to your database, edit the db.py file with the following information:

  • The fully-qualified domain name of the host running the database
  • The database username
  • The database password
  • The name of the database

The information will be in the form:

DATABASE_URL='postgresql://{username}:{password}@{domain name}/{database name}'

For example, if you are running a database called "domdb" on a host called "myserver.whatever.edu" with username "domdbuser" and password "12345", the line in db.py should look like this:

DATABASE_URL='postgresql://domdbuser:12345@myserver.whatever.edu/domdb'

Running

Now run the command line. Specify "neg" or "pos" depending on the ion mode.

python cli.py neg

You should see a prompt like this:

1234 metabolites in database
DOMDB v1
domdb>

You can now run domdb commands.

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