Command Line Support
Flapjack contains a simple command-line option that can be used to pre-create .flapjack project files from existing data files. This ability allows for the creation of project files outwith the Flapjack environment, for instance, to allow a web server (that links to a database) to make Flapjack project files available for download.
The utility is run in a different way depending on the platform used. For all systems excluding Mac OS X, you can use the createproject executable located in the root folder where Flapjack is installed. For Mac OS X, you must manually run the utility using:
java -cp lib/flapjack.jar flapjack.io.CreateProject <options>In all cases, the following options are available:
-map=<map_file> - specifies the location of the file containing map data (required).
-genotypes=<genotypes_file> - specifies the location of the file containing genotype data (required).
-traits=<traits_file> - specifies the location of the file containing trait data (optional).
-qtls=<qtls_file> - specifies the location of the file containing QTL data (optional).
-project=<project_file> - specifies the name of the project file that will be created.
For example:
createproject.exe -map=input.map -genotypes=input.dat -project=output.flapjack
A description of the input file formats accepted is given here. Note also that the project file will be created in compressed XML format, regardless of any selections made within Flapjack itself.