The configuration file

The Disperse software uses a couple of programs and data files not included in the distribution. The configuration file is used to specify the location of these programs and files.

By default, Disperse will use the config file 'config/default_config.properties', but an alternative file may be specified using a command line option. Path entries may be relative or absolute. Relative entries are interpreted relative to the location of the config file itself.

The default entries of the config file use Unix-style pathnames. If installing to a Windows system, use Windows path names, e.g. 'C:\Program Files\Disperse\data\CCDS.20070227.txt'.

Do not use double quotes (") around file names with spaces in them (on Windows systems). Disperse adds quotes, and would be confused if there were quotes already.

Like the settings file, a config file is made up of several property key-value pairs, one per line, such as:

key1=value1
key2=value2

The available properties and their meaning are as follows:

resource.ccdsFile
Location of the CCDS data file to use

Most users will NOT need to change this

resource.masterSnpFile
Location of the SNP data file to use (optional)

Most users will NOT need to change this

resource.blastDb
Location and name of the Blast database (without then .nin or .nal extension) to use

Most users WILL need to change this, depending on the location of the blast data directory.

path.javaExecs
Path to the directory containing the java executable scripts.

Most users will NOT need to change this

path.fastacmd
Path to the fastacmd executable.

Most users WILL need to change this, depending on the location of the blast bin directory.