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)

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.

    1. Binary Database (default) - Recommended

    1. 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