Running FragPipe in headless mode (command line)

For most desktop users, we recommend running FragPipe in GUI mode (https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html). Users can also use FragPipe on remote server with X forwarding (https://fragpipe.nesvilab.org/docs/tutorial_setup_x_forwarding.html).

To run FragPipe in command line, using fragpipe (Linux) or fragpipe.bat (Windows) in fragpipe/bin directory with the following commands:

Running without GUI. Usage:
        Windows: fragpipe.bat --headless --workflow <path to workflow file> --manifest <path to manifest file> --workdir <path to result directory>
        Linux: fragpipe --headless --workflow <path to workflow file> --manifest <path to manifest file> --workdir <path to result directory>
Options:
        -h
        --help                          # Print this help message.
        --headless                      # Running in headless mode.
        --workflow <string>             # Specify path to workflow file.
        --manifest <string>             # Specify path to manifest file.
        --workdir <string>              # Specify the result directory.
        --dry-run                       # (optional) Dry run, not really run FragPipe.
        --ram <integer>                 # (optional) Specify the maximum allowed memory size. The unit is GB. Set it to 0 to let FragPipe decide. Default = 0
        --threads <integer>             # (optional) Specify the number of threads. Default = core number - 1
        --config-msfragger <string>     # (optional) specify the location of the MSFragger jar file. If not specified, using the one in the cache.
        --config-philosopher <string>   # (optional) specify the location of the Philosopher binary file. If not specified, using the one in the cache.
        --config-python <string>        # (optional) specify the location of the Python directory. If not specified, using the one in the cache.

To get the workflow and manifest files, running FragPipe GUI, set the parameters, save the workflow to custom folder, and save the manifest file. These two files can also be edited by any text editor.