At its simplest level, you can run shotmap.pl as follows. The following command invokes all default values in shotmap.
perl $SHOTMAP_LOCAL/scripts/shotmap.pl -i <path_to_input_data> -d <path_to_search_database>
Note that -d points to the path of the ShotMAP formatted search database, not the reference database. For more information, please see section Building a ShotMAP Search Database.
As there are many ways to tune shotmap through the variety of options it provides, it may be simplest to specify your parameters through the use of a configuration file, which is simply a text file that contains a list of the command line parameters you want shotmap to invoke (see section Configuration Files for more information). Generally, most users will NOT need to bother building a configuration file.
perl scripts/build_conf_file.pl --conf-file=<path_to_configuration_file> [options]
perl $SHOTMAP_LOCAL/scripts/shotmap.pl --conf-file=<path_to_configuration_file>
If desired, you override the configuration file settings at the command line when running shotmap:
perl $SHOTMAP_LOCAL/scripts/shotmap.pl --conf-file=<path_to_configuration_file> [options]
If you want to rerun or reprocess part of the workflow (say, with different options), you can jump to a particular step using the --goto option. The command would subsequently look like the following:
perl $SHOTMAP_LOCAL/scripts/shotmap.pl -i <path_to_input_data> -d <path_to_search_database> -o <path_to_output_ffdb> --goto=<goto_value>
For a full list of the values that the --goto option can accept, see the shotmap.pl options documentation.