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.
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.
Platform-specific Notes
This workshop will be using the software outlined in the install instructions below.
Please see the section for your operating system for those directions.
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.
A spreadsheet program For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Windows
should automatically be selected. Click Download Version 4.4.2. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
Putty You will need a terminal program to access the AWS Cloud/HPC cluster.
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
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.
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.
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. (You may need to log in on the login page, but lately the login has not been working.)
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
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.
A spreadsheet program For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Mac
should automatically be selected. Click Download Version 4.4.2. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
FTP Client (Filezilla) An FTP client will help you transfer files easily between your computer and the cloud.
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
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.
Under Installers select RStudio 0.98.1103 - 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.
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. (You may need to log in on the login page, but lately the login has not been working.)
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
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.
A spreadsheet program For this workshop you will need a spreadsheet program. Many people already have
Microsoft Excel installed, and if you do, you're set!
If you need a spreadsheet
program, there are a few other options, like OpenOffice and LibreOffice. Install
instructions for LibreOffice, which is free and open source, are here.
Download the Installer Install LibreOffice by going to the installation page. The version for Linux
should automatically be selected. Click Download Version 4.4.2. You
will go to a page that asks about a donation, but you don't need to make one.
Your download should begin automatically.
Install LibreOffice Once the installer is downloaded, double click on it and it should install.
To use LibreOffice, double click on the icon and it will open.
FTP Client (Filezilla) An FTP client will help you transfer files easily between your computer and the cloud.
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
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.
R is available through most Linux package managers.
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).