Software Carpentry: The Genome Analysis Centre (TGAC)

Registration

Registration for this event is now closed. If you have any queries about upcoming training events, please contact the organisers.

Where: Darwin Room, Norwich Research Park, Norwich, NR4 7UH. Get directions with OpenStreetMap or Google Maps.

Code of Conduct

Software Carpentry and TGAC are committed to ensuring a safe and accessible learning environment for all attendees of all backgrounds. Participants are therefore required to abide by Software Carpentry's Code of Conduct.

Requirements

You will need to bring a laptop with some required software already installed in order to attend the bootcamp. Please let us know as soon as possible if you are not able to bring your own laptop.

The easiest way to get set up with the prerequisites for the bootcamp is to install the preconfigured virtual machine (VM). This VM contains the Linux operating system and all the software needed. As such, we suggest that participants bring their laptop with NoMachine installed.

If you are confident to install the requirements on your own laptop, please follow the setup directions below.

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

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

Windows

Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option. This will provide you with both Git and Bash in the Git Bash program.

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. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

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

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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 (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

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.

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.

Windows

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, or Sublime Text.

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 Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer.
Install Python 3 using all of the defaults for installation.

Linux

Open http://continuum.io/downloads with your web browser.
Click on "I want Python 3.X" link.
Download this Python 3 installer, save it in your home folder.
Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
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).

Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.

Etherpad

During the workshop we will be usign Etherpad to chat, take notes, share URLs, and trace some feedback. You can get to the Etherpad at this page.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Arrival	Pre-workshop Survey
09:00	Welcome and Software set up
09:30	Part 1: Using the shell to do more in less time
10:30	(Coffee Break)
11:00	Part 2: Using the shell to do more in less time
12:30	(Lunch)
13:30	Part 1: Using version control to manage and share information
15:00	(Coffee Break)
15:30	Part 2: Using version control to manage and share information
16:00	Part 1: Python and good programming practice
17:00	End of day

Day 2

09:00	Recap and questions
09:30	Part 2: Python and good programming practice
10:30	(Coffee Break)
11:00	Using Python for scientific programming
12:30	(Lunch)
13:30	Debugging and testing
15:00	(Coffee Break)
15:30	Final Exercises
16:30	Wrap up
Dismissal	Post-workshop Survey