How-to-install.md

+
+The scripts in this repository coded in Python,
+but use several dependencies which can be installed by the following
+instructions.
+
+All the required packages should work on any platform and on linux based systems.
+The code has been tested in Python v.3.8
+
+Install dependencies with conda (all platforms)
+-----------------------------------------------
+
+This is the recommended way to install all the dependencies. 
+
+**Prerequisites**
+
+You should have a recent version of the [conda](https://docs.conda.io/en/latest/)
+package manager. You can get [conda](https://docs.conda.io/en/latest/) by installing
+[miniconda](https://docs.conda.io/en/latest/miniconda.html), if you want a light version of the package manager.
+
+**Conda environment**
+
+Once conda is installed on your system you can easily create a fixed python environment
+to use in every run by:
+
+~~~
+conda create --name sst_env python=3.8
+~~~
+
+Then activate it:
+~~~
+conda activate sst_env
+~~~
+
+To install the code dependencies you must have activated your environment. You
+will know is activated once you see the name of the environment (e.g sst_env)
+in () at the beginning of your bash alias:
+
+~~~
+(sst_env) [brecinos@jasmin-sci2 ~]$
+~~~
+
+Make sure conda-forge channel is your default channel to install dependencies:
+
+~~~
+conda config --add channels conda-forge
+~~~
+
+To install dependencies simply do:
+
+~~~
+conda install -c conda-forge numpy pyreadr pandas xarray scipy cartopy pyproj configobj seaborn
+~~~
+
+We then need to install [netCDF4](https://github.com/Unidata/netcdf4-python) and the library [salem](https://salem.readthedocs.io/en/stable/), to use such libraries we need to install some dependencies with pip:
+
+~~~
+pip install shapely rasterio Pillow geopandas netcdf4 scikit-image joblib motionless dask descartes
+~~~
+
+Now we can install netCDF4 and joblib:
+
+~~~
+conda install -c conda-forge netCDF4 joblib
+~~~
+
+Finally, we can install salem:
+
+~~~
+pip install git+https://github.com/fmaussion/salem.git
+~~~
+
+If you want to run the jupyter-notebooks in the repository make sure you also install those tools in your environment:
+
+~~~
+conda install -c conda-forge ipykernel
+~~~
+
+You can add to your jupyter notebook installation a kernel to select this environment every time you activate the notebook.
+
+~~~
+python -m ipykernel install --user --name sst_env --display-name "sst_env"
+~~~
+
+
+**Install the repository itself**
+----------------------------------
+
+For this to work you'll need to have the [git](https://git-scm.com/) software installed on your system. Then, clone the latest repository version:
+
+~~~
+git clone git@git.noc.ac.uk:brecinosrivas/orchestra-sst.git
+~~~
+
+If you are inside [JASMIN](https://help.jasmin.ac.uk/article/185-generate-ssh-key-pair),
+you might have to configure your **Gitlab** ssh keys (under **Gitlab Profile >> Settings > Ssh keys**).
+ And add a JASMIN pub key to your profile (generated from within a JASMIN's sci-server).
+ This in order to enable access from JASMIN sci servers to your NOC gitlab platform and
+ to clone the repository within one of JASMIN's sci servers.
+
+ For more information on gitlab ssh keys [click here](https://git.noc.ac.uk/help/ssh/README.md).