Update 'README.md'

README.md

@@ -29,7 +29,7 @@ https://brodeau.github.io/barakuda/example/
   => https://www.enthought.com/products/canopy/
 
   In any case, specify the appropriate "PYTHON_HOME" environment variable in
-  your ${BARAKUDA_ROOT}/configs/config_<MYCONF>.sh or ./config_<MYCONF>.sh file
+  your ${BARAKUDA_ROOT}/configs/config_${MYCONF}.sh or ./config_${MYCONF}.sh file
 
 * NEMO output data! => A directory containing the MONTHLY-AVERAGED, global
                        (rebuilt), NEMO output to analyze
@@ -39,7 +39,7 @@ https://brodeau.github.io/barakuda/example/
   XIOS2 can be found in: src/xios2_xml/
 
 * a NEMO mesh_mask file and the the corresponding basin_mask (ocean basins).
-  (variables MM_FILE and BM_FILE into the config_<MYCONF>.sh file you use).
+  (variables MM_FILE and BM_FILE into the config_${MYCONF}.sh file you use).
   
   To create the NEMO mesh_mask.nc just launch the relevant NEMO experiment with the
   namelist parameter nn_msh set to 1 !
@@ -63,7 +63,7 @@ https://brodeau.github.io/barakuda/example/
 
 
 
-### I / Compile CDFTOOLS executables 
+### I/ Compile CDFTOOLS executables 
 
  * CDFTOOLS is a set of FORTRAN executables intended to perform a multitude of
    ocean diagnostics based on NEMO output
@@ -95,21 +95,21 @@ https://brodeau.github.io/barakuda/example/
 
            
 
-### II / Create and configure your own "config_<MY_CONF>.sh"
+### II/ Create and configure your own "config_${MYCONF}.sh"
 
 All setup related to your host, simulation, location of third party files is
-defined in the "config_<MY_CONF>.sh" file.
+defined in the "config_${MYCONF}.sh" file.
 
 You can either used to chose a config file located in the
 "${BARAKUDA_ROOT}/configs" directory of Barakuda:
-('${BARAKUDA_ROOT}/configs/config_<MY_CONF>.sh')
+('${BARAKUDA_ROOT}/configs/config_${MYCONF}.sh')
 
 Or, in case you have no write access into ${BARAKUDA_ROOT}/ and call the Barakuda
 suite of scripts from another location, hereafter "work directory", you can use
-a "config_<MY_CONF>.sh" present in the "work directory".
+a "config_${MYCONF}.sh" present in the "work directory".
 
-Note: if a given "config_<MY_CONF>.sh" exists both in "${BARAKUDA_ROOT}/configs"
-and the "work directory", Barakuda will always refer to "config_<MY_CONF>.sh"
+Note: if a given "config_${MYCONF}.sh" exists both in "${BARAKUDA_ROOT}/configs"
+and the "work directory", Barakuda will always refer to "config_${MYCONF}.sh"
 present in the "work directory".
 
 IMPORTANT: Always refer to the most relevant
@@ -118,14 +118,17 @@ yours! These are symbolic links pointing to the last officially supported and
 most up-to-date config files.  It should be sufficiently well commented for you
 to be able to adjust your own config file.
 
+```
 MY_CONF should always be of the form: "(e)ORCA<RES>_L<NLEV>_<blabla>.sh"
         ( with NLEV being the number of z levels )
+```
 
 NEMO output files must be monthly averages and of the following form:
-
+```
         <EXP NAME>_1m_<YEAR>0101_<YEAR>1231_<GRID_TYPE>.nc(.gz)
 
         (GRID_TYPE=grid_T/grid_U/grid_V/icemod) 
+```        
 
 Gzipped or not!
 
@@ -154,8 +157,7 @@ The "CONF_INI_DIR" variable in your config file should point to the location of
 the directory you created by untaring one of these tar archives.
 
 
-
-### III) Create diagnostics
+### III/ Create diagnostics
 
 
 Launch "barakuda.sh"
@@ -173,22 +175,26 @@ Use the -h switch to see available options.
 * Once the previous job has finished to run, launch
 
 To only generate time-series plots use the "-e" switch:
-
+```
         ./barakuda.sh -C <MY_CONF> -R <EXP> -e
 
         (ex: ./barakuda.sh -C ORCA1_L75_v36_triolith -R SL36C00 -e)
+```        
 
 To generate time-series + 2D climatology plots use the "-E" switch, provided you
 have built the monthly/annual climatology (based on N years of your simulation)
 out of your experiment with the "build_clim.sh" script (see next bullet point):
-     
+```     
         ./barakuda.sh -C <MY_CONF> -R <EXP> -E
+```        
 
 * To be able to create the "climatology" plots (maps, sections, etc, based on a monthly climatology of a few years) you will have to
 
   1. create the climatology with the "build_clim.sh" script:
 
+```
         ./build_clim.sh -C <MY_CONF> -R <EXP> -i <first_year> -e <last_year>
+```        
 
     Use the -h switch to see available options.
       
@@ -197,8 +203,9 @@ out of your experiment with the "build_clim.sh" script (see next bullet point):
 
 
 * To compare time-series between at least 2 (already diagnosed) experiments:
-   
+```   
          ./compare_time-series.sh -C <MY_CONF> -R <EXP1>,<EXP2>,...,<EXPn>
+```         
 
          (ex: ./compare_time-series.sh -C ORCA1_L75_v36_triolith -R SL36C00,SL36EIE )