Overview

BioNetDB implements the bionetdb.sh command line with the following syntaxis:

bionetdb.sh [-h|--help] [--version] <command> [options]

General Usage Documentation

In this section you will learn how to use the command lines, some examples are provided using bionetdb.sh command line.

Basic Command Line Conventions

BioNetDB follows the most standard conventions when implementing command lines, the most relevant ones are:

• single-character parameters start with only one hyphen symbol and can be either lower-case or upper-case, e.g. -h to print the help or -S to provide session id; while multi-character parameters start with two hyphens and are always lower-case, e.g. --help to print the help or --name to provide a name.
• in the Usage the optional parameters are written always between [ square brackets ], in the following example help, version and option are not mandatory:

      ./opencga.sh [-h|--help] [--version] <command> [options]

• in the Usage the mandatory parameters are written between symbols < and >, like <command> in the previous example.

Executing the command line

You can execute the command line without any argument to get the usage help (you can also provide -h parameter):

Program:     BioNetDB (OpenCB)
Version:     1.0.0
Description: BioNetDB implements a storage engine to work with biological networks using Neo4j, a NoQSL Graph database

Usage:       bionetdb.sh [-h|--help] [--version] <command> [options]

Commands:
              import  Import the built data models in format CSV files into the database
              query  Query and fetch data from BioNetDB database using this command line