Mar 23-24, 2015
9:00 am - 5:00 pm
Instructors: Ivan Gonzalez, Meeta Mistry
Helpers: Radhika Khetani, Mary Piper
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 part of the NGS Data Analysis Course (Spring 2015).
Contact: Please mail firstname.lastname@example.org for more information.
Pre-workshop office hours: We are holding office hours to help those who find problems installing the required software on Friday, March 20th (room 438B in HSPH building 2, this is the preferred option) and from 8:30 am to 9 am on workshop's first day. You need to schedule your slot here.
Files: Please download these files for the corresponding lessons: shell.
|09:00||Automating tasks with the Unix shell|
|13:00||Version control with Git|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
In addition to what is described below, you will need to install other software for the reminder of the NGS Data Analysis course.
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.
This installer requires an active internet connection.
After Git Bash:
Information about the SWC Windows Installer, including the source code, can be found at https://github.com/swcarpentry/windows-installer.
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.