Configuration Flags

These are the flags for the configuration process of EnTAP. These will be used via the command line (denoted CMD), entap_run.params file (denoted R-ini), or entap_config.ini file (denoted E-ini).

There are a few data types (qualifiers) to keep in mind used throughout these ini files. Anything that is specifies as a ‘multi’ type means that the parameter may be entered multiple times. If it is in an ini file, each parameters must be separated by a comma (‘,’). Example for multi-integer:”1,2,3” (entered without quotes)

Required/Recommended Flags

param	description	location (cmd/R-ini,E-ini)	qualifier	example
config	Must be specified in order for EnTAP to run Configuration as opposed to normal execution	cmd	flag	config
run-ini	Point to the entap_run.params to specify database paths to be configured for DIAMOND, thread usage, and more.	cmd	string	/path/to/entap_run.params
entap-ini	Point to the entap_config.ini to specify database paths to prevent redownloading and DIAMOND executable in order to format FASTA databases for DIAMOND.	cmd	string	/path/to/entap_config.ini
eggnog-map-data	Specify the output directory for the EggNOG database (eggnog.db). EnTAP will check for the eggnog.db database within this specified directory. If it is not there, it will be redownloaded. So set this to prevent duplicate downloads!	E-ini	string	/path/to/eggnog_database_directory
eggnog-map-dmnd	Specify the filepath to the eggnog_proteins.dmnd EggNOG database. EnTAP will check this path for the database. If it does not exist, it will be downloaded. So set this to prevent duplicate downloads!	E-ini	string	/path/to/eggnog_proteins.dmnd
entap-db-bin	Path to the entap_database.bin database. Either this or the EnTAP SQL database must be used. The binary database is the default and is recommended. EnTAP will check for this path during Configuration. If it is not there, it will be redownloaded. So set this to prevent duplicate downloads!	E-ini	string	/path/to/entap_database.bin
diamond-exe	Specify the execution method for DIAMOND. This can be a path to the diamond file generated during installation, or simply the command if installed globally. Used to configure databases for EnTAP to use during Similarity Searching	E-ini	string	diamond
database / d (optional)	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). Additionally, you can specify the type of database you’d like EnTAP to download and configure for use with DIAMOND using any of the following flags: refseq_archaea, refseq_bacteria, refseq_complete, refseq_fungi, refseq_invertebrate, refseq_other, refseq_plant, refseq_protozoa, refseq_vertebrate_mammalian, refseq_vertebrate_other, ncbi_nr, uniprot_sprot, uniprot_trembl	R-ini	multi-string	/path/to/diamond/database
threads / t	Specify thread number	R-ini	number	4
out-dir	Specify the output directory for databases (EnTAP, DIAMOND, EggNOG) to be written to	R-ini	string	/path/to/entap_output

Optional Flags

param	description	location (cmd/R-ini,E-ini)	qualifier	example
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.	R-ini	bool	true
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.	R-ini	multi-number	0
entap-db-sql	Path to the entap_database.db database. Either this or the EnTAP binary database must be used. EnTAP will check for this path during Configuration. If it is not there, it will be redownloaded. So set this to prevent duplicate downloads!	E-ini	string	/path/to/entap_database.db