The scanps_defaults.dat contains settings for valid commands. When you first install scanps, you will have to modify this file to define the correct locations for your directories. For example:
DB_DIR /gjb/delly/databases/scanps/ MATRIX_DIR /gjb/delly/gjb/c/scanps/gjscanps/mat/ GENERAL_DIR /gjb/delly/gjb/c/scanps/gjscanps/dat/ MATRIX_FILE PAM250 MAX_NSEQ 5000000 CODON_FILE codon.dat MATRIX_FILE nmd.mat MAX_NSEQ 500000 MAX_SEQ_LEN 400000 LD_PEN 1 LI_PEN 8 DB_FORMAT 0
This defines the directories for various files. See the specific command summary below for further details.
Commands in the scanps_defaults.dat file may either be the full command name or an alias as defined in the scanps_alias.dat file (see below). Usually, it is best to use the full command name in the scanps_defaults.dat file. Aliases are there to ease typing commands on the command line. Note that ALL commands and their aliases are case sensitive.