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 13 so vmdk file is osgeolive-13.0-amd64.vmdk.7z. The osgeolive-13.0-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-13.0-amd64.vmdk.7z. A this point you are ready to load the osgeolive-13.0-amd64.vmdk inside Virtualbox.

Install OSGeoLive inside Virtualbox

Lunch Virtualbox from OS and follow the below instructions.

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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:

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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 redo the procedure.

Open the bash terminal (green icon in the down left corner) 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

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

Another test that you should do it is to test 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 /home/user/.local/share/cartopy/shapefiles/natural_earth/physical/ne_110m_land.shp

You should see the openev software popup and ope the the tif and shp files.

Test R studio

rstudio

You should see the rstudio software pop-up

Setting Python Virtual Env.

$ sudo apt-get install python3-venv $ python3 -m venv pyVenv

change line in ~/pyVenv/pyvenv.cfg
-------------------------------------------------------------------------------
include-system-site-packages = false --> include-system-site-packages = true
-------------------------------------------------------------------------------

$ pip install -U pip $ pip install jupyterlab

Git Settings

First time action

These lines download the folder data ‘SE_data’ from github. If you do not have the folder ‘/home/user/SE_data’ proceed with the download. If you have already the folder it will prompt an error: ‘fatal: destination path ‘SE_data’ already exists and is not an empty directory’.

cd 
git clone https://github.com/selvaje/SE_data.git 
cp -r SE_data /media/sf_LVM_shared/my_SE_data

The same procedure can be used for restore the full SE_data folder.

Future routine

setup

~/SE_data : server copy, sync. with cloud

/media/sf_LVM_shared/my_SE_data : working copy, for yourself, always work here.

Proceed with these lines every time we have new class material.

cd ~/SE_data
git pull # synchronise with cloud  
rsync -hvrPt --ignore-existing ~/SE_data/* /media/sf_LVM_shared/my_SE_data # local sync.
cd /media/sf_LVM_shared/my_SE_data

starting working here.