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Install_and_Configure.md

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Installation and configuration

The source code can be downloaded from the GitHub repository. MATLAB should be installed, and some tasks will requre cygwin (for the bash shell), Campbell Scientific's CardConvert utility, and R tobe installed and on the path.

Local machine setup

Data and configuration directories

NMEG_Fluxproc scripts and functions reqire access to a local data directory (FLUXROOT) and a configuration file directory (FluxProcConfig). On the local machine, MATLAB must be able to find these two directories.

FLUXROOT

The NMEG_FluxProc scripts and functions performs operations on data in a designated path (termed FLUXROOT). An example FLUXROOT directory with data from an imaginary site can be downloaded from the socorro ftp and used to test the NMEG_FluxProc code.

FluxProcConfig

Site specific configuration files must also be present in the FLUXROOT path, and NMEG_FluxProc is currently set to look for them in FLUXROOT/FluxProcConfig. Configuration files for NMEG sites, including the test site mentioned above can be found [here] (https://github.com/gremau/NMEG_FluxProcConfig).

Paths and environment variables.

An environment variable must be set for MATLAB to find the FLUXROOT (and FluxProcConfig) directory on the local machine's file structure. In your startup.m file, add these lines:

setenv('FLUXROOT', '/.../')

where "/.../" is the path to the FLUXROOT directory. This will add the needed environment variable each time you start MATLAB.

Once this is done, start MATLAB, add the NMEG_FluxProc to your path:

addpath('path/to/FluxProc')

Enter the directory:

cd 'path/to/FluxProc'

The rest of the paths needed for FluxProc can be set using

fluxproc_setpaths

Now NMEG_FluxProc code should be initialized and ready to use the data and configuration files in the FLUXROOT directory.