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Add full setup instructions to Git setup
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biologyguy committed Dec 21, 2017
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<a href="https://help.github.com/articles/keeping-your-email-address-private/">these instructions</a>
for keeping your email address private.
</p>
</div> <!-- End of 'Git' section. -->
</div> <!-- End of 'Git' section. -->

<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
the workshop will teach Python using something other than
the IPython notebook.
Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
<h3>Python</h3>

<p>
<a href="http://python.org">Python</a> is a popular language for general-purpose
programming that has been widely adopted for scientific computing. Unfortunately, installing all of
its scientific packages individually can be difficult, so we will be relying on an
all-in-one installer called <a href="https://www.continuum.io/anaconda">Anaconda</a>.
</p>
<p>
<strong>For all instructions below, please ensure you install Python version 3</strong>
</p>

<div class="row">
<div class="col-md-4">
<h4 id="python-windows">Windows</h4>
<!-- <a href="https://www.youtube.com/watch?v=xxQ0mzZ8UvA">Video Tutorial</a> -->
<ol>
<li>Open <a href="https://conda.io/miniconda.html">https://conda.io/miniconda.html</a> with your web browser.</li>
<li>Download the Python 3 installer for Windows.</li>
<li>Install Python 3 using all of the defaults for installation. Make sure the
<strong>Register Anaconda as my default Python</strong> checkbox is selected before clicking 'Install'.</li>
</ol>
</div>
<div class="col-md-4">
<h4 id="python-macosx">Mac OS X</h4>
<!-- <a href="https://www.youtube.com/watch?v=TcSAln46u9U">Video Tutorial</a> -->
<ol>
<li>Open <a href="https://www.continuum.io/downloads">https://www.continuum.io/downloads</a> with your web browser.</li>
<li>Download the Python 3 installer for OS X.</li>
<li>Install Python 3 using all of the defaults for installation.</li>
</ol>
</div>
<div class="col-md-4">
<h4 id="python-linux">Linux</h4>
<ol>
<li>Open <a href="https://conda.io/miniconda.html">https://conda.io/miniconda.html</a> with your web browser.</li>
<li>Download the Python 3 installer for Linux.</li>
<li>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.)</li>
<li>
Open a terminal window.
</li>
<li>
Type <pre>bash Miniconda3-</pre> and then press
tab. The name of the file you just downloaded should
appear.
</li>
<li>
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 <code>yes</code> and
press enter to approve the license. Press enter to approve the
default location for the files. Type <code>yes</code> and
press enter to prepend Anaconda to your <code>PATH</code>
(this makes the Anaconda distribution the default Python).
</li>
</ol>
</div>
</div>
</div> <!-- End of 'Python' section. -->

<div id="shell"> <!-- Start of 'shell' section. -->
<h3>The Bash Shell, Jupyter, and Git</h3>
<ul>
<li>Bash is a commonly-used shell that gives you the power to do simple
tasks more quickly.</li>
<li>Git is a version control system that lets you track who made changes
to what and has options for easily updating a shared or public
version of your code
on <a href="https://github.com/">github.com</a>.</li>
<li>We will teach Python using the Jupyter 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
<a href="http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility">supported</a>
(some older browsers, including Internet Explorer version 9
and below, are not).</li>
</ul>

<div class="row">
<div class="col-md-4">
<h4 id="shell-windows">Windows</h4>
<ol>
<li>Open a command prompt
<ul><li>Open Start Menu </li>
<li>type <code>cmd</code></li>
<li>press [Enter]</li></ul>
</li>

<li>
Type the following lines into the command prompt window one at a time exactly as shown, hitting [Enter]
after each one.
<pre>
conda create -n bash m2-base git jupyter pandas tornado=4.4 console_shortcut

activate bash

conda install -c swc nano</pre>

Continue to press [Enter] at any prompts and wait for the 'C:\' to return after
each command before progressing (<strong>the first step can take many minutes
and look like it's stuck, so please be patient</strong>).
</li>

<li>
You should now be able to find a new folder in your Start menu called 'Anaconda'. Inside the folder will
be two 'Anaconda Prompt' programs. Choose the one that doesn't say '(bash)'
</li>
<li>Activate the correct conda environment by typing:
<pre>activate bash</pre>
</li>
</ol>
<br/>Optionally, <a href="http://cmder.net/">Cmder</a> is a (much) nicer terminal environment for Windows.
</div>
<div class="col-md-4">
<h4 id="shell-macosx">Mac OS X</h4>
<p>
The default shell in all versions of Mac OS X is Bash.
</p>
<ol>
<li>Open the 'Terminal' program (found in <code>/Applications/Utilities</code>).</li>
<li>Type the following into the Terminal command prompt window exactly as shown:
<pre>conda install git jupyter pandas</pre></li>
</ol>
<br/>Optionally, <a href="https://www.iterm2.com/">iTerm2</a> is a more feature-rich terminal environment that is
a little easier on the eyes.
</div>
<div class="col-md-4">
<h4 id="shell-linux">Linux</h4>
<p>
The default shell is usually Bash, but if your machine is set up
differently you can run it by opening a terminal and typing <code>bash</code>.
</p>
<ol>
<li>Open the Terminal</li>
<li>Type the following into the command prompt window exactly as shown:
<pre>conda install git jupyter pandas</pre></li>
</ol>
</div>
</div>
</div> <!-- End of 'shell' section. -->

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