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Setup
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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

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.

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