: Setup

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they’re working. If you have any problems, don’t hesitate to email the instructors to ask for help, or arrive early on the first day to get help.

Windows

Putty

You will need a terminal program to access the remote machine. This is already available on Mac and Linux.

Go to the Putty download page
Click on putty.exe link to download the install file
To use it, double-click on the download file
Follow the installation instructions, if any

R

Install R by downloading and running this .exe file from CRAN
Also, please install RStudio
After starting RStudio, at the console type: install.packages(c(“tidyverse”, “RSQLite”))

MacOSX

R

Install R by downloading and running this .pkg file from CRAN
Also, please install RStudio
After starting RStudio, at the console type: install.packages(c(“tidyverse”, “RSQLite”))

Linux

R

You can download the [binary files for your distribution] from CRAN or you can use your package manager (e.g. for Debian/Ubuntu run
```
 sudo apt-get install r-base
```
and for Fedora run
```
 sudo yum install R
```
Also, please install RStudio
After starting RStudio, at the console type: install.packages(c(“tidyverse”, “RSQLite”))

Linux, Windows and Mac

FTP Client (Filezilla)

An FTP client will help you transfer files easily between your computer and the cloud.

Go to the Filezilla download page
Chose the download link appropriate to your system
To use it, double-click on the downloaded file
Follow any installation instructions, if any
At the workshop we will give you additional information (e.g. host, username, port) to connect

Chrome

Go to the Chrome download page
Click and the button and install Chrome

IGV

We will use The Broad Institute’s IGV (Integrated Genome Viewer) for looking at SAM and BAM files, SNPs, and variant calls.

To download IGV, please visit this page and log in
Click on the large button for the Download Binary Distribution
Find the zip archive on your computer and expand it
To run IGV, double-click on the IGV.bat file.