#Setting up Bioinformatic Environment in Windows

I installed Windows 7 (64-bit) to mimic CICSE environment for teaching. I will attempt to set up environment in a way that will work for the course.

##Git for Windows
Based on Software Carpentry recommendations will ...

>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.


<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Git_for_Windows_-_Windows_Internet_Explorer_1BB99C85.png" alt="Git_for_Windows_-_Windows_Internet_Explorer_1BB99C85.png"/>

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<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Release_Git_for_Windows_2_5_3_·_git-for-windows_git_·_GitHub_-_Google_Chrome_1BB99DAD.png" alt="Release_Git_for_Windows_2_5_3_·_git-for-windows_git_·_GitHub_-_Google_Chrome_1BB99DAD.png"/>

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I left everything as default during installation except ....
<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Git_2_5_3_Setup_1BB99E76.png" alt="Git_2_5_3_Setup_1BB99E76.png"/>

Make sure to select *Use Windows default console window*


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Play around... 
From start menu selected Git Bash. 
It is not pretty, but `pwd`, `ls`, work

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/MINGW64__c_Users_sr320_Desktop_1BB99F45.png" alt="MINGW64__c_Users_sr320_Desktop_1BB99F45.png"/>

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Opening Git Gui opens this Window

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/Git_Gui_1BB99F97.png" alt="Git_Gui_1BB99F97.png"/>


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Will install GitHub Desktop as this mimics what I am used to on Mac.

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/GitHub_Desktop_-_Google_Chrome_1BB99FED.png" alt="GitHub_Desktop_-_Google_Chrome_1BB99FED.png"/>

First fail.

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/System_Update_Required_1BB9A08A.png" alt="System_Update_Required_1BB9A08A.png"/>

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Did a Windows update..

seems fine.

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/GitHub_1BB9B5FB.png" alt="GitHub_1BB9B5FB.png"/>

Going to set-up new repo (for safety)

<img src="http://eagle.fish.washington.edu/cnidarian/skitch/GitHub_1BB9B6E5.png" alt="GitHub_1BB9B6E5.png"/>


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<img src="http://eagle.fish.washington.edu/cnidarian/skitch/GitHub_1BB9B82B.png" alt="GitHub_1BB9B82B.png"/>