Data Carpentry Workshop Setup Instructions

Requirements: Data Carpentry's teaching is hands-on, so participants are encouraged to bring in and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop. (We will provide instructions on setting up the required software several days in advance) There are no pre-requisites, and we will assume no prior knowledge about the tools.

Contact: Please email admin@datacarpentry.org for questions and information not covered here.

Setup

To participate in a Data Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything and try opening it to make sure it works before the start of your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.

Windows
Mac
Linux

Windows

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 of the workshop to get help.

R
In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
- Download R from here
- Run the .exe file that was just downloaded
- Go to the RStudio Download page
- Under Installers select RStudio 0.98.1103 - Windows XP/Vista/7/8
- Double click the file to install it
- Once it's installed, open RStudio to make sure it works and you don't get any error messages.
Putty
You will need a terminal program to access the HPC cluster.
- 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
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
IGV
If time permits, 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.

Mac

R
In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
- Go to CRAN and click on Download R for (Mac) OS X
- Select the .pkg file for the version of OS X that you have and the file will download.
- Double click on the file that was downloaded and R will install
- Go to the RStudio Download page
- Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) to download it.
- Once it's downloaded, double click the file to install it
- Once it's installed, open RStudio to make sure it works and you don't get any error messages.
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
IGV
If time permits, 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.

Linux

R
In the workshop, we will use RStudio. RStudio is a nice interface to the programming language R. To use RStudio, you need to install both R and RStudio.
- Follow the instructions for your distribution from CRAN. For most distributions, 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) but make sure that you have at least R 3.2.2 (as pre-packaged versions might be out of date).
- To install RStudio, go to the RStudio Download page
- Under Installers select the version for your distribution.
- Once it's downloaded, double click the file to install it (or sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
- Once it's installed, open RStudio to make sure it works and you don't get any error messages.
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
IGV
If time permits, 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.