Required System Software
This workshop requires that the following software be installed and tested before the workshop:
| Name/Link | Description | Additional Requirements |
|---|---|---|
| 1. R | Most popular analysis program in statistical genetics | Yes (Specific Libraries). |
| 2. Python 3. | Multi purpose Programming Language | Yes (The matplotlib library). |
Both popular computer languages, R and python3 will be used during the workshop. Here we will provide a guide for installation of both languages and their associated libraries.
1. R (and associated packages)
R is the most popular analysis program in statistical genetics, and required for most genetic analysis. We recommend that MacOS users download an up-to-date (4.4.1)
version directly from the R website and using the R installer. If you are having trouble we recommend this video tutorial.
While Linux users can also find a suitable version on the website, we recommend using the package installer that comes with Debian based distributions (Debian, Ubuntu, Mint, etc) and downloading R directly using the following terminal commands:
sudo apt install r-base # to install R
sudo apt install build-essential # to install the essential packages
Important: Additional R Packages Are Required
This workshop requires the following non-standard R packages: BEDMatrix, boot, data.table, doMC, glmnet, MASS, optparse, parallel, and R.utils These packages can be installed by opening up an R session from within the terminal, by typing:
R
And typing the following command:
install.packages(c("BEDMatrix","boot","data.table","doMC","glmnet","MASS","optparse","parallel","R.utils"))
After you have finished installation and testing of R, please consider completing our R-tutorial to better familiarize yourself with some basic analysis commands.
2. Python3 (and matplotlib)
Python3 is a popular multiuse programming language. This workshop requires Python3 and the matplotlib library. Any version of Python3 is acceptable but a newer version Python3.10.10+ is recommended.
Many systems come installed with Python3 by default, but it can be downloaded from the python website. The matplotlib package can be found here.
Users of macOs can find detailed instructions on how to install python3 by visiting the following video link that we find very helpful. After installing python3, macOs users can install matplotlib using pip:
python3 -m ensurepip
sudo python3 -m pip install -U matplotlib
For Linux we again recommend that you use the package installer to install python3 and matplotlib
sudo apt install python3 # to install python3
python3 --version # to verify that it worked
sudo apt-get install python3-matplotlib # to install matplotlib
After you have finished with this section, don't forget to complete our Python tutorial to familiarize yourself with some basic commands.