Jan 29-30, 2015
9:00 am - 4:30 pm
Instructors: Karen Cranston, Darren Boss
Helpers: Christian Gunning, Daniel Rotroff, Megan Fritz
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. Early registration will go through Wednesday January 14th at 5pm. During this early registration period, registration is restricted to the Departments of Entomology, Plant Pathology, and the Biotechnology Program at NCSU. Post-docs will be given priority. Please contact Megan Fritz (see below) for a registration password.
Beginning January 15th, registration will open up to all NCSU post-docs, faculty, staff and graduate students.
Where: Teaching and Visualization Lab, 4th floor, James B Hunt Jr Library, 1070 Partners Way, Raleigh, NC. Get directions with OpenStreetMap or Google Maps.
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 mlfritz@ncsu.edu for more information or to obtain a registration password.
Support This workshop is possible partly due to donation of instructor time from the National Evolutionary Synthesis Center (Karen Cranston) and the Duke Center for Genomic and Computational Biology (Darren Boss).
09:00 | Automating tasks with the Unix shell |
10:30 | Coffee |
12:00 | Lunch break |
13:00 | Building programs with Python |
14:30 | Coffee |
16:00 | Wrap-up |
09:00 | Version control with Git |
10:30 | Coffee |
12:00 | Lunch break |
13:00 | Managing data with SQL |
14:30 | Coffee |
16:00 | Wrap-up |
Etherpad: https://etherpad.mozilla.org/2015-01-29-ncsu.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
add
, commit
, ...status
, diff
, ...clone
, pull
, push
, ...where
join
This page has instructions on testing that you have the right software installed. Note the five sections: Text Editor, Bash Shell, Git, Python and SQLite. If you have problems installing any of the software, please arrive early (between 8 am and 9 am) and we'll get you sorted out!
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
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.
We recommend
Text Wrangler or
Sublime Text.
In a pinch, you can use nano
,
which should be pre-installed.
Kate is one option for
Linux users. In a pinch, you can use nano
, which
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.
This installer requires an active internet connection.
After installing Python and 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
(found in
/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
install anything.
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
the installer.
After installing Git, there will not be anything in your /Applications
folder,
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
OS available
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
.
Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.
We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yes
and
press enter to approve the license. Press enter to approve the
default location for the files. Type yes
and
press enter to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Download the sqlite3 program and put it in the directory where you are running examples.
sqlite3
comes pre-installed on Mac OS X.
sqlite3
comes pre-installed on Linux.