mako

CLI Overview

The CLI has been separated in several modules for ease of use. Selecting a module is done by including the module name in the script call, like so:

  • mako base
  • mako neo4biom
  • mako io
  • mako netstats
  • mako metastats
  • mako manta
  • mako anuran

For learning more about the parameters used by each module, type mako module -h in your terminal, replacing module with the name of the module you are interested in. In the next sections, a brief overview of module functionalities is provided.

Several parameters are present across all modules. These provide information necessary to access the Neo4j database. By setting the -cf flag, Neo4j access information only needs to be stored once as mako will generate a config file that can be accessed. This is not a protected file, so this should not be used when addressing highly secured databases. However, for local Neo4j Desktop and Docker instances, the config file saves repeated entry of details.

  • -fp File path for reading / writing files and log
  • -cf Use flag to store Neo4j access information
  • -u Neo4j username
  • -p Neo4j password
  • -a Neo4j address
← Introduction
mako base →