Data, Code and Computational Environment for: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion
Authors/Creators
- 1. Aristotle University of Thessaloniki
- 2. Hellenic Agricultural Organization (ELGO) DIMITRA
- 3. Kostelenos Olive Nurseries
Description
Data
The csv file "2023-06-27_data.csv" contains genetic profiles for all olive trees analyzed in the publication: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion". The genotypes are provided in the GenAlEx format.
Code
Code is provided in the compressed folder "Tourvas_et_al_Olive". It is structured as a R project and can easily be opened, after decompressing, from the Rstudio interface. If you prefer to review and/or reuse code you can access it from the "analysis" folder inside the "Tourvas_et_al_Olive" folder.
Computational Environment
A tarball for the Docker image "tourvas_et_al_olive" is also provided. This is the recommended way to reproduce the results of the publication: "Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion".
It is assumed that you already have Docker installed on your system. If not, please visit https://docs.docker.com/get-started/
To use it:
- download the image file tourvas_et_al_olive.tar
- load it with docker with the command:
docker load --input tourvas_et_al_olive.tar- then launch the Docker container with the command:
docker run --name popgen --rm -dp 8787:8787 -e ROOT=TRUE -e DISABLE_AUTH=true -v "`pwd`":/home/rstudio/working nikostourvas/tourvas_et_al_olive- start your favorite web browser and go to: http://localhost:8787/
- from the bottomright pane of the Rstudio server click on the directory "Tourvas_et_al_Olive" and open the project by clicking on the "Tourvas_et_al_Olive.Rproj" file
- launch the scripts inside the "analysis" directory and run them to reproduce results