Prepare OSGeoLive for Spatial Ecology courses

In order to execute the Spatial Ecology exercise we will need first install the OSGeoLive Linux Virtual Machine and then populate with additional software and data.

OSGeoLive is a self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu, that allows you to try a wide variety of open source geospatial software without installing anything. It is composed entirely of free software, allowing it to be freely distributed, duplicated and passed around (source https://live.osgeo.org/en/index.html)

You can follow the below instructions, moreover the OSGeoLive installation YouTube video can guide along the full procedure.

For running a Virtual Machine in your OS we need a virtualization software such as Virtualbox and a vmdk file that contains the virtualized OS.

Install Virtualbox

Open you browser and go to https://www.virtualbox.org/wiki/Downloads and base on your OS download the Virtualbox executable and install it.

Download OSGeoLive

Open you browser and go to https://sourceforge.net/projects/osgeo-live/files/. Click on the last version-folder and proceed to download the osgeolive-??.0-amd64.vmdk.7z. At the time of writing the last version is 14 so vmdk file is osgeolive-14.0-amd64.vmdk.7z. The osgeolive-14.0-amd64.vmdk.7z is a quite large file therefore according to your Internet connection it can take several hours. When the download is finished unzipped using 7zip. Mac users can use The Unarchiver for unzip the osgeolive-14.0-amd64.vmdk.7z. A this point you are ready to load the osgeolive-14.0-amd64.vmdk inside Virtualbox.

Install OSGeoLive inside Virtualbox

Lunch Virtualbox from OS and follow the below instructions.

Test your OSGeoLive Virtual Machine

If you follow all the steps correctly the OSGeoLive Virtual Machine you should pop-up in the Virtual Box window showing something like this:

Setting you keyboard layout

If are not use the US keyboard you have to add your keyboard layout to the bottom menubar. Therefore on the left bottom corner write “keyboard” in the search box, and select Keyboard and Mouse.

Then select “Keyboard Layout” > “Add” and select your keyboard layout in accordance to your country and language.

Your keyboard layout will appear as below. Move up to select it as default keyboard layout.

Open the terminal (black icon in the down left corner of the menubar, close to the firefox icon) and test if the keyboard layout is correct.

Screen size/resolution of your OSGeoLive Virtual Machine

If the screen is very small try to enlarge, and if the enlargement is not working properly try to reboot. Sometime the Virtual Box guest edition is not kick-in so you have to do the procedure dscribed below.

Open the bash terminal and run line by line the following codes. The sudo password is “user”. For security what you type is not shown, anyway it is recorded. After typed the password press enter.

Update the OS. This operation can last few minutes. Be patient. If during the installation, some screen pop-up asking some question just accept the default option.

sudo apt update      # update the repositories
sudo apt upgrade -y  # installation of the sw

Add to Virtualbox additional add-on to improve the graphical user interface of the VM. If during the installation some screen pop-up asking some question just accept the default option.

From the Virtualbox menu press Device > Insert Guest Addition CD image

The download procedure will start and a screen will pop up:

press “insert”, and if the below screen pop up

pres “cancel”.

Open the terminal and type:

cd /media/user/VBox_GAs_*
sudo ./VBoxLinuxAdditions.run

At this point you can reboot your machine. Now all screen setting, screen scale and drag/drop should work properly.

Test your shared folder

Another test that you should do, is to see if the shared folder is correctly done. Open a bash terminal and run

ls /media/sf_LVM_shared

If are able to list the folder then means that the sharing folder operation is properly done. Moreover try to insert a file from your host OS in the LVM_shared folder and see if visible in the OSGeoLive.

If you get an error “ls: cannot access ‘/media/sf_LVM_shared’: No such file or directory” means that you did not correctly done the sharing folder operation so try to redo it.

Populate OSGeoLive with additional software

At this point the OSGeoLive Virtual Machine is ready to install additional software and data for running Spatial Ecology courses. In the bash terminal run the following lines

cd /tmp/
wget https://raw.githubusercontent.com/selvaje/SE_data/main/exercise/install_additional_sw_data_4SE_courses.sh
sudo bash ./install_additional_sw_data_4SE_courses.sh

as before the sudo password is “user”.

Test installed additional software

In the bash terminal run the following lines one by one. Close the window that each time pop-up.

Test pktools

pkfilter --help

You should see the pkfilter manual instructions

Test OpenEV

source ~/.bashrc
openev /home/user/jupyter/notebook_gallery/Rasterio/data/world.rgb.tif

You should see the openev software popup and open the the tif file.

Test R studio

rstudio

You should see the rstudio software pop-up

Git Settings

The below instructions together with the Git Setting for the Spatial Ecology courses YouTube video can guide along the full procedure to retrive dataset and material for the courses.

The folder data ‘SE_data’ from github will be download and you see under ‘/home/user/SE_data’. If you have already the folder it will prompt an error: ‘fatal: destination path ‘SE_data’ already exists and is not an empty directory’.

Below the same commands for an easy copy-paste

cd ~/SE_data
#### git clone https://github.com/selvaje/SE_data  ## only run the first time
git pull                                           ## run every 5min before each lecture
rsync -hvrPt --ignore-existing ~/SE_data/* /media/sf_LVM_shared/my_SE_data

Now you should be ready to follow the lectures of the Spatial Ecology courses. Remember always to work on

cd /media/sf_LVM_shared/my_SE_data

Settings for running jupyterlab

The below instructions are needed to create a python virtual environment (in this case juplab_env) that need to be activate via “source ~/juplab__env/bin/activate” everytime that you wanna use jupyterlab

sudo apt install python3.8-venv
python3 -m venv juplab_env
## allow to use system python packages
sed 's/false/true/g' ~/juplab_env/pyvenv.cfg > ~/juplab_env/pyvenv_tmp.cfg ;
mv ~/juplab_env/pyvenv_tmp.cfg ~/juplab_env/pyvenv.cfg

source ~/juplab_env/bin/activate    ### run this line everytime wanna use jupyterlab
pip install -U pip
pip3 install jupyterlab