Configuration Flags

These are the flags for the configuration process of EnTAP. These will be used via the command line (denoted CMD) or ini file (denoted INI).

Required Flags

param	description	location (cmd/ini)	qualifier	example
config	Must be specified in order for EnTAP to run Configuration as opposed to normal execution	cmd	flag	config
ini	Point to the entap_config.ini to specify paths. DIAMOND is only required for Configuration.	cmd	string	/path/to/entap_config.ini

Optional Flags

param	description	location (cmd/ini)	qualifier	example
database / d	Specify any number of FASTA formatted databases you would like to configure for EnTAP. Not necessary if you already have DIAMOND configured databases (.dmnd extension)	cmd	multi-string	/path/to/diamond/database
threads / t	Specify thread number	cmd	number	4
out-dir	Specify the output directory for databases (EnTAP, DIAMOND, EggNOG) to be written to	cmd	string	/path/to/entap_output
data-generate	Specify this flag if you would like to generate EnTAP databases rather than downloading from FTP (default). Only needed if you are having issues connecting to FTP.	cmd	flag	data-generate
data-type	Specify which EnTAP database you’d like to generate/download. There are two provided in case there are any compatibility issues across platforms. Binary Database (default) - Recommended SQL Database - Slower although may resolve certain compatibilty issues across systems with low available memory This can be used multiple times to download/configure multiple databases at once.	ini	multi-number	0