add explanation for roothpath

Author: SarahAlidoost

_episodes/03-configuration.md

@@ -9,7 +9,82 @@ objectives:
 keypoints:
 - "First key point. Brief Answer to questions. (FIXME)"
 ---
-FIXME
+
+## The configuration file
+
+The ``config-user.yml`` configuration file contains all the global level
+information needed by ESMValTool to run. This is an (YAML file) [https://yaml.org/spec/1.2/spec.html]. An example configuration file can be found in the root directory of the ESMValTool repository.
+Make a copy and rename it to ``config-user.yml``.
+
+~~~
+  cp config-user-example.yml config-user.yml
+~~~
+{: .source}
+
+This file contains:
+  * Rootpaths to the data from different projects
+  * Directory structure for input data
+  * Number of available CPUs
+  * Destination directory
+  * Auxiliary data directory
+  * Output settings
+
+## Rootpaths to input data
+ESMValTool uses several categories (in ESMValTool, this is referred to as projects) for input data based on their source, like CMIP for dataset from climate model intercomparison project, OBS for observational dataset that adhere to (CMOR standard)[https://cmor.llnl.gov/]
+For each category, you can define either one path or several pathes as a list.
+Add the root path of the folder where you downloaded the data during the (Setup)[https://escience-academy.github.io/lesson-esmvaltool/setup.html]
+
+~~~
+  rootpath:
+  ...
+    CMIP5: [~/cmip5_inputpath1, ~/cmip5_inputpath2, ~/escience-academy/test_data]
+~~~
+{: .source}
+
+## Auxiliary data directory (used for some additional datasets)
+  auxiliary_data_dir: ~/auxiliary_data
+
+The ``auxiliary_data_dir`` setting is the path to place any required
+additional auxiliary data files. This method was necessary because certain
+Python toolkits such as cartopy will attempt to download data files at run
+time, typically geographic data files such as coastlines or land surface maps.
+This can fail if the machine does not have access to the wider internet. This
+location allows us to tell cartopy (and other similar tools) where to find the
+files if they can not be downloaded at runtime. To reiterate, this setting is
+not for model or observational datasets, rather it is for data files used in
+plotting such as coastline descriptions and so on.
+
+
+## Output settings
+
+.. code-block:: yaml
+
+  # Diagnostics create plots? [true]/false
+  write_plots: true
+  # Diagnositcs write NetCDF files? [true]/false
+  write_netcdf: true
+
+The ``write_plots`` setting is used to inform ESMValTool about your preference
+for saving figures. Similarly, the ``write_netcdf`` setting is a boolean which
+turns on or off the writing of netCDF files.
+
+The ```rootpath`` specifies the directories where ESMValTool will look for input
+data. Similarly, ``output_dir`` specifies where ESMValTool will store its
+output, i.e. figures, data, logs, etc. Make sure to set appropriate paths.
+
+.. code-block:: yaml
+
+
+
+
+You can tailor it for your system using the explanation below.
+
+.. note::
+
+   The ``config-user.yml`` file is specified as argument at run time, so it is
+   possible to have several available with different purposes: one for
+   formalised runs, one for debugging, etc...
+
 
 {% include links.md %}