Software Carpentry: GCB Academy - Introduction to Scientific Computing for Genomics

GCB Academy - Introduction to Scientific Computing for Genomics

Feb 05-06, 2015

9:00 am - 5:00 pm

Instructors: Darren Boss (GCB), Karen Cranston (National Evolutionary Synthesis Center), Hilmar Lapp (GCB), Dan Leehr (GCB), Scott White (Department of Biostatistics and Bioinformatics)

Helpers: Dan Somers (GCB), Darrin Mann (GCB)

General Information

Computing has become an integral and indispensable part of genomic biology. This course teaches basic skills in scientific computing, with a focus on applications for genomic science, aimed at making you more productive, your computational work more reliable, and your research easier to reproduce and extend, including by your future self. The course includes introductions to

using Unix shell commands to efficiently find, organize, and stage data for analysis;
basic data types, control flows, functions, and 3rd party packages for the Python programming language commonly encountered in scientific computing;
using version control to manage with confidence the numerous directions research code takes from inception to publication; and
techniques for optimizing how your computational analyses run on a high-performance computing cluster.

The format of the course is inspired by the acclaimed Software Carpentry-style bootcamps. Hence, this is a fully hands-on workshop, and students are expected to bring a laptop.

Who: The course is aimed at graduate students, postdocs, early career faculty, and other researchers.

Where: Bostock Library, Workshop Room in The Edge. 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 gcb-help@duke.edu for more information.

Schedule

Day 1

09:00	Automating tasks with the Unix shell
10:30	Coffee
12:30	Lunch break
13:30	Building programs with Python
15:00	Coffee
17:00	Wrap-up

Day 2

09:00	Version control with Git
10:30	Coffee
12:30	Lunch break
13:30	Job and data staging for HPC
15:00	Coffee
16:00	Wrap-up

Etherpad: https://etherpad.mozilla.org/Clo0hBRMky.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Setup

This page has instructions on testing that you have the right software installed.

Text Editor

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.

In this workshop, for the sake of consistency across systems we will be standardizing on the nano editor, which is a basic editor that is integrated into the lesson material.

Windows

nano is installed by the Software Carpentry Installer.

Another popular free code editor for Windows is Notepad++. 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).

Mac OS X

nano should be pre-installed.

We also recommend Text Wrangler or Sublime Text.

Linux

nano should be pre-installed.

We also recommend Kate.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection.

After installing Python and Git Bash:

Download the installer.
If the file opens directly in the browser select File→Save Page As to download it to your computer.
Double click on the file to run it.

Rsync client

Download the Grsync installer and double click on the file to run it. Grsync for Windows.

Mac OS X

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.

Linux

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

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.

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

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.

Linux

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

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.

Windows

Download and install Anaconda.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Download and install Anaconda.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Linux

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.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type 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).