This section describes advanced usage of GenMAPP by computer programmers. GenMAPP may be integrated with other programs through the GenMAPP command line. Using the command line you can specify a number of parameters for GenMAPP, such as the MAPP to open, the Gene Database and Expression Dataset to use, the Color Set and the MAPP Set to create and where to store it. The primary program invocation for a typical installation would be:
"C:\Program Files\GenMAPP 2\GenMAPPv2.exe"
Command-line parameters, each enclosed in its own set of quotes, may follow the primary invocation. To specify a MAPP to open when the program starts, put the MAPP's path after the primary invocation:
"C:\Program Files\GenMAPP 2\GenMAPPv2.exe" "C:\GenMAPP 2 Data\MAPPs\glycolysis.mapp"
Parameters other than MAPPs, Expression Datasets, and Gene Databases may be stated but each must have a code that allows GenMAPP to determine which parameter is being set The codes are as follows:
| Code | Meaning | Example |
| path.mapp | MAPP Path | "C:\GenMAPP 2 Data\MAPPs\glycolysis.mapp" |
| path.gdb | Gene Database | "C:\GenMAPP 2 Data\Gene Databases\Hs-Std_20030823.gdb" |
| path.gex | Expression Dataset | "C:\GenMAPP 2 Data\Expression Datasets\MyExperiment.gex" |
| colors:|colorsets| | Color Set | "colors:|2-wk|4-wk|8-wk|" A Color Set parameter is ignored if no Expression Dataset is stated. For MAPP Sets, you may state multiple Color Sets delimited by pipes. A single Color Set may be stated without pipes. Multiple Color Sets, only allowable for MAPP Sets, must be surrounded by pipes. "colors:None" indicates no Color Set but is the same as leaving out the colors: parameter. "colors:All" indicates all Color Sets for MAPP Sets. |
| set:folder | MAPP Set | "C:\GenMAPP 2 Data\MAPPs\MyMAPPSet" The MAPP set parameter is the root path for the MAPPs exported into the MAPP Set. The set consists of all the MAPPs in this folder and its subfolders. |
| dest:folder | Destination path for MAPP Set | "C:\GenMAPP 2 Data\Exports" |
To create a MAPP Set with a specific Gene Database, Expression Dataset, and Color Set, you might use this invocation:
"C:\Program Files\GenMAPP 2\GenMAPPv2.exe" "C:\GenMAPP 2 Data\Gene Databases\Hs-Std_20030823.gdb" _ "C:\GenMAPP 2 Data\Expression Datasets\MyExperiment.gex" "colors:|2-wk|4-wk|8wk|" _ "set:C:\GenMAPP 2 Data\MyMAPPs\MyMAPPSet" "dest:C:\GenMAPP 2 Data\Exports"