Although not required it is recommended to set up a configuration for the DomainWorld program suite. It is recommended because it will make the usage of programs easier. However, all parameters can be given as arguments to the different programs as well.

By default, the configuration file is assumed to be in ${Home}/.domainWorld, if you prefer a different directory you can set the DOMAINWORLD_DATA environment variable to point to the directory you have chosen.

Have a look at this example file: general.conf

You will probably need some additional data, depending on which program(s) you plan to use (have a look at the programs website to see what is needed). At the end your folder structure should look similar to this:

├── dsm
│   └── pfam-30.dsm
│   └── pfam-31.dsm
└── general.conf

1 directory, 3 files