Basic Flags¶
These are the general flags that can be used during Configuration. These will be used via the command line (denoted CMD) or ini file (denoted INI).
-d / --database [string] [CMD]¶
- Specify any number of FASTA formatted databases you would like to configure for EnTAP
- Not necessary if you already have DIAMOND configured databases (.dmnd)
--out-dir [string] [CMD]¶
- Specify an output directory for the databases to be sent to (recommended)
- This will send the EnTAP database and DIAMOND databases to this location
-t / --threads [number] [CMD]¶
- Specify thread number for Configuration
--data-generate [CMD]¶
- Specify this flag is you would like to generate the EnTAP database rather than downloading from FTP (default)
- I’d only use this if you’re having issues with the FTP
--data-type [flag] [INI]¶
Specify which databases you’d like to generate/download
- Binary Database (default) - This will be much quicker and is recommended
- SQL Database - Slower although will be more easily compatible with every system
This can be flagged multiple times (ex: - - data-type 0 - - data-type 1)
I would not use this flag unless you are experiencing issues with the EnTAP Binary Database