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+# Contributing New Material
+
+Data Carpentry is an open source project, and we welcome contributions of all
+kinds: new and improved lessons, bug reports, and small fixes to existing
+material are all useful.
+
+By contributing, you are agreeing that Data Carpentry may redistribute your
+work under [these licenses](LICENSE.md).
+
+
+**Table of Contents**
+
+* [Working With GitHub](#working-with-github)
+* [Locations and Formats](#locations-and-formats)
+* [FAQ](#faq)
+
+
+## Working With GitHub
+
+1. Fork the `datacarpentry/lesson-name` repository on GitHub.
+
+2. The default branch in our lessons is `gh-pages`. Create a
+ new branch for your changes.
+ Give your branch a meaningful name,
+ such as `fixing-typos-in-shell-lesson`
+ or `adding-tutorial-on-visualization`.
+
+3. Clone this repository and branch to work with it on your computer.
+ git clone the repository with -b 'branch name'
+
+4. Make your changes, commit them, and push them to your repository on GitHub.
+
+5. Send a pull request to the `gh-pages` branch of the main datacarpentry
+ repository at http://github.com/datacarpentry/lesson-name. This can
+ be done through the github web interface.
+
+If it is easier for you to send them to us some other way,
+please mail us at
+[board@datacarpentry.org](mailto:board@datacarpentry.org).
+Given a choice between you creating content or wrestling with Git,
+we'd rather have you doing the former.
+
+
+## Locations and Formats
+
+Every lesson has a repository of its own, while individual topics are files
+in that directory. For example, the `shell-ecology` directory holding our
+introduction to the shell for ecology contains the files `00-intro.md`,
+`01-filedir.md` and so on. (We use two digits followed by a one-word topic
+key to ensure files
+appear in the right order when listed.)
+
+Lessons may be written in Markdown, as IPython Notebooks, or in other formats.
+However, as explained in [the README file](README.md), Jekyll (the tool GitHub
+uses to create websites) only knows how to handle Markdown and HTML. if some
+other format is used, the author of the lesson must add the generated Markdown
+to the repository. This ensures that people who *aren't* familiar with some
+format don't have to install the tools needed to work with it (e.g., R
+programmers don't have to install the IPython Notebook).
+
+> If a lesson is in a format we don't already handle, the author must also add
+> something to the Makefile to re-create the Markdown from the source. Please
+> check with us if you plan to do this.
+
+
+## Formatting of the material
+
+To ensure a consistent formatting of the lessons, we recommend the following
+guidelines:
+* No trailing white space
+* Wrap lines at 80 characters (unless it breaks URLs)
+* Use unclosed atx style headers (see below)
+
+## FAQ
+
+* *Where can I get help?*
+
+
+
Setting Up
+
+
+ This workshop may require some software installation, and details will be included here.
+
+
+
+
+
+
Windows
+
+
+ Download and install
+
+
+
+
+
+
+
+
+
+
Mac OS X
+
+
+ Download and install
+
+
+
+
+
+
+
+
+
+
+
Linux
+
+
+ Download and install
+
+
+
+
+
+
+
+
+
+
Setting Up 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.
+
+
+
+ Regardless of how you choose to install it,
+ please make sure you install Python version 2.x and not version 3.x
+ (e.g., 2.7 is fine but not 3.4).
+ Python 3 introduced changes that will break some of the code we teach during the workshop.
+
+
+
+ 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
+
+
+ Download and
+ install Anaconda .
+
+
+ Download the default Python 2 installer (do not follow the link to version 3).
+ Use all of the defaults for installation
+ except make sure to check
+ Make Anaconda the default Python .
+
+
+
+
+
+
+
+
Mac OS X
+
+
+ Download and
+ install Anaconda .
+
+
+ Download the default Python 2 installer (do not follow the link to version 3).
+ Use all of the defaults for installation.
+
+
+
+
+
+
+
+
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.
+ Download the default Python 2 installer (do not follow the link to version 3).
+
+
+ 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).
+
+
+
+
+
+
+
R
+
+
+ R is a programming language
+ that is especially powerful for data exploration, visualization, and
+ statistical analysis. To interact with R, we use
+ RStudio .
+
+
+
+
+
+
+
Linux
+
+ You can download the binary files for your distribution
+ from CRAN . Or
+ you can use your package manager (e.g. for Debian/Ubuntu
+ run sudo apt-get install r-base and for Fedora run
+ sudo yum install R). Also, please install the
+ RStudio IDE .
+
+
+
+
Overview
+
+
+
+
Editor
+
+ When you're writing scripts or text, 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. (This will lose any unsaved changes to the file.)
+
+
The Bash Shell
+
+ Bash is a commonly-used shell. Using a shell gives you
+ more power to do more tasks more quickly with your
+ computer.
+
+
+
+
R
+
+ R is a programming language that specializes in statistical
+ computing. It is a powerful tool for exploratory data analysis. To
+ interact with R, we will
+ use RStudio , an interactive
+ development environment (IDE).
+
+
SQL
+
+ SQL is a specialized programming language used with databases.
+ We use a simple database manager called SQLite ,
+ either directly or through a browser plugin.
+
+
OpenRefine
+
+ OpenRefine (formerly Google Refine) is a powerful tool for exploring and working with messy data.
+
+
+
+
Windows
+
+
+
+
Editor
+
+ 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.
+
+
Git Bash
+
+ Install Git (version control) and a Bash shell for Windows from
+ the msysGit project's homepage .
+ This will provide you with Bash in the Git Bash program.
+
+
Software Carpentry Installer
+
Other tools used in Data Carpentry have been packaged up by
+ Software Carpentry in an installer. This installer requires an active internet connection.
+
+
+ Download the installer .
+
+
+ Double click on the file to run it.
+
+
+ Accept all defaults.
+
+
+
+
+
R
+
+ Install R by downloading and running
+ this .exe file
+ from CRAN .
+ Also, please install the
+ RStudio IDE .
+
+
SQLite
+
+ Install the Firefox SQLite browser plugin described below .
+
+
OpenRefine
+
+ Download the OpenRefine software described below .
+
+
+
Mac OS X
+
+
+
+
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.
+
+
Editor
+
+ We recommend
+ Text Wrangler or
+ Sublime Text .
+ In a pinch, you can use nano,
+ which should be pre-installed.
+
+
+
+
R
+
+ Install R by downloading and running
+ this .pkg file
+ from CRAN .
+ Also, please install the
+ RStudio IDE .
+
+
SQLite
+
+ sqlite3 comes pre-installed on Mac OS X.
+ Also install the Firefox SQLite browser plugin described below .
+
+
OpenRefine
+
+ Download the OpenRefine software described below .
+
+
+
Linux
+
+
+
+
Bash
+
+ 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.
+
+
Editor
+
+ Kate is one option for Linux users.
+ In a pinch, you can use nano,
+ which should be pre-installed.
+
+
+
+
R
+
+ You can download the binary files for your distribution
+ from CRAN . Or
+ you can use your package manager, e.g. for Debian/Ubuntu
+ run apt-get install r-base. Also, please install
+ the
+ RStudio IDE .
+
+
SQLite
+
+ sqlite3 comes pre-installed on Linux.
+ Also install the Firefox SQLite browser plugin described below .
+
+
OpenRefine
+
+ Download the OpenRefine software described below .
+
+
+
Miscellaneous
+
+
+
+
Firefox SQLite Plugin
+
+ Instead of using sqlite3 from the command line,
+ you may use this plugin
+ for Firefox instead.
+ To install it:
+
+
+
+ Start Firefox.
+
+
+ Go to the plugin homepage .
+
+
+ Click the "Add Now" button.
+
+
+ Click "Install Now" on the dialog that appears after the download completes.
+
+
+ Restart Firefox when prompted.
+
+
+ Select "SQLite Manager" from the "Tools" menu.
+
+
+
+
+
OpenRefine
+
+ Head to the OpenRefine download page for information on how to install it. It will run through a browser, but will not need to use an internet connection, and your data will also be securely stored on your own computer.
+
+
+
+
Spreadsheets
+
+
+ Spreadsheets are useful for data entry and data organization, and
+some subsetting and sorting of the data as well as getting an overview of the data. To interact with spreadsheets, we can use
+ LibreOffice ,
+ Microsoft Excel ,
+ Gnumeric ,
+ OpenOffice.org , or other programs.
+ Commands may differ a bit between programs, but general ideas for thinking about spreadsheets is the same.
+
+
+For this lesson, if you don't have a spreadsheet program already, you can use LibreOffice . It's a free, open source spreadsheet program.
+
+
+
+
Windows
+
+
+ Download the Installer
+ installation page . The version for Windows
+should automatically be selected. Click Download Version 4.4.2 . You
+will go to a page that asks about a donation, but you don't need to make one.
+Your download should begin automatically.
+ Install LibreOffice
+
+
+
+
+
+
Mac OS X
+
+
+ Download the Installer
+ Download Version 4.4.2 . You
+will go to a page that asks about a donation, but you don't need to make one.
+Your download should begin automatically.
+ Install LibreOffice
+ LibreOffice_4.4.2_MacOS_x86-64 should have been downloaded. Double click on this file, and LibreOffice will be installed.
+
+
+
+
+
+
+
+
Linux
+
+
+ Download the Installer
+ Download Version 4.4.2 . You
+will go to a page that asks about a donation, but you don't need to make one.
+Your download should begin automatically.
+ Install LibreOffice
+
+
+
+
+
+
+
+
{{ page.title }}
+ {% endif %}
+ {% include header.html %}
+
+ {% include banner.html %}
+
+
+
+
+ {% if page.title %}
+
{{page.title}}
+ {% endif %}
+ {{content}}
+
+
+
+
+ {% include footer.html %}
+
{{page.title}}
+ {{ page.title }}
+ {% else %}
+ {{ page.venue }}
+ {% endif %}
+ {% include header.html %}
+
+
+ {% include banner.html %}
+
+
+
+
+
A Data Carpentry Workshop
+ Organized by ...
+ {{page.venue}}
+ {% if page.address %}{{page.address}}
+
+
+
+ {{content}}
+
+ {% include footer.html %}
+
+
Twitter : @datacarpentry
+
+