April 18-19, 2015
9:00 am - 5:00 pm
Instructors: Naupaka Zimmerman, Nichole Bennett, Rayna Harris, Kate Hertweck
Helpers: Richard Adams, Heath Blackmon, Daren Card
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Who: The course is aimed at graduate students and other researchers.
Contact: Please mail firstname.lastname@example.org for more information.
|09:00||Scripting your analyses with R|
|13:00||Automating tasks with the Unix shell|
|09:00||Version control with Git|
|13:00||Reproducible research workflows with R|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.
nano is the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.
Kate is one option for
Linux users. In a pinch, you can use
should be pre-installed.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
It installs and configures
nano (Among other things)
This installer requires an active internet connection.
After installing Git Bash:
The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
The default shell is usually
bash, but if your
machine is set up differently you can run it by opening a
terminal and typing
bash. There is no need to
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.7) use the
most recent available installer for your
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.