In the console.
conda activate domainator
domainator_server
It will give you an address, for example:
http://127.0.0.1:44651
You can copy that into your web browser to get a page that looks like:
Download and unzip the Pfam hmm profiles.
https://www.ebi.ac.uk/interpro/download/Pfam/
Upload them to your Domainator GUI by dragging the file to "Choose Files" in the top right, or clicking "Choose Files" and then navigating to the location of the Pfam file.
You can also download individual Pfam profiles from their profile page, for example: https://www.ebi.ac.uk/interpro/entry/pfam/PF24174/logo/
Domainator can operate on Fasta files or GenBank files.
One way to get sequence files is with the Domainator DB Download app.
You can follow along in the GUI with the command line examples:
domainator_server [-h] [--port PORT] [--host HOST] [--data-dir DATA_DIR] [--schema-dir SCHEMA_DIR] [--debug]
Start the Domainator web server
options:
-h, --help show this help message and exit
--port PORT Port to bind the server. By default, a random free port is chosen. (default: 0)
--host HOST Host interface to bind. Defaults to localhost. To make the server accessible on the network, use
0.0.0.0 (default: 127.0.0.1)
--data-dir DATA_DIR Data directory for uploads, jobs, and logs. Defaults to /home/sean/domainator_server (default: None)
--schema-dir SCHEMA_DIR
Directory containing tool and workflow schema JSON files (default: None)
--debug Enable Flask debug mode (default: False)