Jan 26 - 27, 2015
9:00 am - 4:30 pm
Instructors: Naupaka Zimmerman, Nichole Bennett
Helpers: John Caskey, Nick Maggio, Hani Nakhoul, Tina O'Grady, Joon Ro, Travis White
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; 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, postdocs, faculty and other researchers in the Tulane Cancer Center and BMS program.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
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||Pulling it all together - automation and reproducible research|
To participate in a Software Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.
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.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
Git is a state-of-the-art version control system. It 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.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection
After installing Python and Git Bash:
nano is the editor installed by the Software Carpentry Installer,
it is a basic editor integrated into the lesson material.
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.
The default shell in all versions of Mac OS X is bash,
so no need to install anything. You access bash from
the Terminal (found
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager, e.g. for Debian/Ubuntu
apt-get install r-base or
yum install R.
Also, please install the