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The few minutes it takes to optimize your workflow will be the best few minutes you will spend in CSE 330 and your career. It is remarkable how many hours you can save just by using the best interface for text editing and deployment.


There are going to be several aspects to our workflow in CSE 330, and we will be switching between multiple different programs. Here is how they all fit together.

Running Commands

Mac OS X: You will be running commands on your local machine using Terminal, which you can find in your Applications -> Utilities folder. You will be connecting to your server via SSH also in Terminal.

Windows: You will be running commands on your local machine using Cygwin, which you will install in the next section. You will be connecting to your server via SSH also in Cygwin.

Version Control

You will be using SourceTree as a frontend to the Git version control system. Git enables you to keep track of changes to your source code, and also push your changes up to the CEC.

Text Editing

You will be using Komodo Edit as your text editing tool. Komodo Edit will also enable you to upload files to your Amazon cloud instance.


If you are more visual, this flowchart might help:


The flowchart illustrates 3 methods to copy files to your cloud instance: via your text editor, via an external SFTP client, and by cloning your remote Git repository. We will be primarily using Option 1 in CSE 330 this semester.

In the flowchart, your Git Client is SourceTree and your Text Editor is Komodo. The optional SFTP Client could be FileZilla.


Cygwin is a Linux Terminal emulator for Windows.

Mac OS X users do not need to install Cygwin since OS X itself is a derivative of Unix, which is an ancestor of Linux. The Terminal utility is all you need.


The CEC lab machines already have Cygwin installed. Follow these instructions to get Cygwin up and running on your personal PC.

  1. Run setup.exe from
  2. Keep the Cygwin directory as the default, C:\cygwin. Choose a place like C:\cygwin\downloads to download the installation files. Choose any download site, although probably one with a .com suffix is best when you're in the US.
  3. In the "Select Packages" screen, select the following packages:
    • Net -> openssh
    • Net -> openssl
    • Python -> python (you will need this for Module 4)
    • One or more of the following:
      • Editors -> vim
      • Editors -> emacs
      • Editors -> nano
  4. Allow the installation to complete.

Throughout the rest of this course, when we say to "open a terminal", if you are on Windows, we mean to "open Cygwin".


SourceTree is a tool that enables you to perform version control using a graphical user interface. It is free and available for Windows 7+ and Mac OS X 10.6+.

SourceTree is available on the Mac App Store. Windows users (and OS X users who don't like the App Store) may install it from


Git is a distributed version control system that enables you to track changes to your code and work with collaborators on the same code base. In CSE 132, you used Subversion (SVN), which is also version control system.

Git, like SVN, is a command-line tool. However, SourceTree enables you to use Git without having to pull up a Terminal window every time you need to perform an action.

In Module 5, you will learn more advanced techniques for using Git. However, for Modules 2-4, you will be using Git primarily as a method to push your changes to your remote repository.

Configuring Git/SourceTree

Once you install SourceTree, you need to tell it your name so that it knows how to tag changes you make.

  1. Open the SourceTree Preferences (SourceTree->Preferences on OS X or Tools->Options on Windows).
  2. Check the box that says "Allow SourceTree to modify your global Mercurial and Git configuration files".
  3. Enter your name and e-mail address.
    Note: This actually does the same thing as running git config --global <NAME HERE> and git config --global <EMAIL HERE> from the command line.
  4. Finally, go to the "Git" tab in the preferences and uncheck "Use the staging area".
    You will learn about staging in Git in Module 5, but for Modules 2-4 we will skip the staging area.

Cloning a Repository

Screenshot of cloning a repository in SourceTree

We will start by cloning a remote Git repository.

"Cloning" in Git is much like "checking out" in SVN: a remote copy of the repository is copied down to a local working directory. Word of Caution: Git uses the term "checkout" to mean something different (which you will learn in Module 5), so do not use the words "clone" and "checkout" interchangeably.

If you wanted to clone a repository on the command line, the command would be:

$ git clone git:// destination-path

In SourceTree, go to File->New, enter the remote repository URL and the destination path, and press "Clone". The destination path is where you want the repository's files to be copied on your personal computer; the path should point to either an empty or a nonexistent directory on your personal computer. In the screenshot, I am cloning the repository for the Fedora Linux kernel.

The remote repository will now be cloned onto your personal computer and all ready to use.


Screenshot of committing to a repository in SourceTree

When you make changes to files or add new files, you need to commit them to your working repository. Note: When you "commit" something in SVN, it means that you are sending your changes to the remote repository. This is not the case in Git, as we will see shortly.

To prepare your commit, press the "Commit" button in the SourceTree toolbar. See the screenshot for an example.

Select the files you want to commit, and enter a commit message summarizing the changes you've made since your last commit. When you're ready, press "Commit".

The command line equivalent of this would be:

$ git add --all # adds untracked files to the repository and stages them for the commit
$ git commit -am "This is an example commit"

What happens now is that your changes are recorded in your own local working copy of the Git repository. The changes have not been saved in the remote repository. You need to do this by pushing them.


Git is different from SVN in that you can use it completely independently from a remote repository. Thus, in Git, you need to perform the "commit" and "push" steps separately.

After you perform a commit, you need to push your commit to your remote repository. To do this, press the "Push" button in SourceTree, and then press "OK". The command line equivalent is:

$ git push master # assuming your branch is still named the default "master"

Note: You do not need to push after every commit. You could have 4 or 5 commits before you actually perform the push. When you push, all commits will be pushed.


In SVN, if you want to download changes from your remote repository, you performed an update. In Git, you perform a pull.

Pulling is (usually) as simple as pressing the "Pull" button in SourceTree. The command line equivalent is:

$ git pull master

Note: If you want to download the changes from the remote repository but not overwrite your current working copy, you can perform a fetch instead.

Pageant and PuTTYgen: SSH Keys for Windows

Pageant is a Windows utility that enables applications like SourceTree and Komodo Edit (which we will install in the next step) to be able to use your SSH keys when authenticating on remote services (like your EC2 instance). PuTTYgen is a utility that converts SSH keys into a format that Pageant can understand.

Mac OS X and Linux users may skip this section.

Installing Pageant and PuTTYgen

Pageant and PuTTYgen both come bundled with SourceTree, so you do not need to install them separately. However, if you weren't using SourceTree, you could install them from:

Using PuTTYgen

We will use PuTTYgen to convert our SSH keys into Pageant's format, *.ppk.

  1. Launch PuTTYgen. If you downloaded puttygen.exe, just open it; if you are using the SourceTree version, you can find it under the Tools menu:
  2. Inside PuTTYgen, click "Load" next to "Load an existing private key file". We want to load the private key we generated in the SSH guide using ssh-keygen. If you kept Cygwin's default file structure, you should be able to find the key at:
    C:\cygwin\home\<your name>\.ssh\id_rsa
    Note that you might need to choose "All Files (*.*)" in order to see the file.
  3. When the key gets loaded, click "Save private key"
    You may use a passphrase if you want, but it is not required for CSE 330
  4. Save the new file in a secure location where you will always be able to access it.
  5. Close PuTTYgen.

Using Pageant

To launch Pageant, either run pageant.exe or select it from the Tools menu in SourceTree:


The first time you launch pageant, it will ask you to select a key. Select the *.ppk file you saved in the previous section.

If you wish to add more keys to Pageant, right-click on its icon down in the start bar:


Adding Pageant as a Startup Item

If you are using your own computer, it may be convenient to add Pageant as a startup item so that you don't need to go into SourceTree and turn it on every time you reboot your computer.

  1. Download pageant.exe if you were using SourceTree
  2. Open your Startup Items folder, located at Start Menu -> All Programs -> Startup (right-click and say "Open")
  3. Right-click inside the folder and say "New -> Shortcut". For the location, enter:
    "C:\path\to\pageant.exe" "c:\path\to\key.ppk"
    This will cause Pageant to open and automatically load your key.
  4. Press "Next". Enter a name and press "Finish".

Thanks to the University of Alberta for this tip.

Komodo Edit


This semester in CSE 330, we will be using Komodo Edit as our editor of choice. We chose this editor because:

  1. It is free for everyone.
  2. It runs on Windows, Mac OS X, and Linux.
  3. It supports all of the languages we will be using in this class.
  4. It has a decent amount tools like auto-completion that will speed up your workflow.


Komodo Edit is already installed on the CEC lab machines. If you prefer to use your personal computer, download it from the web site:

Connecting Komodo to your Remote Instance

With a little time spent on configurations and installing a plugin, Komodo Edit enables you to edit files on your desktop and then upload those files directly to your remote instance.

Configure your Server Settings in Komodo

Once you have your public key in your SSH agent (if applicable), follow these steps to tell Komodo how to connect to your remote instance.

  1. Open the Komodo Edit Preferences. In Windows, this is Edit -> Preferences; in Mac OS X, this is Komodo -> Preferences.
  2. In the menu on the left, choose Servers.
  3. For Server Type, select SFTP. (Since you have an SSH server running, you will be able to connect to your instance via SFTP.)
  4. Name it something like CSE 330 Cloud Instance.
  5. Enter the details of your instance, including your hostname and username.
    • If you are using Public Key Authentication, leave your password empty.
    • Unless you explicitly changed your SSH port, your port will be 22.
  6. Your default path will be where you want to save the files you upload. Generally, this should be the root of your web server.
  7. Press Add to save the server information, and then press OK.
  8. Mac OS X Users Only: You need to perform these additional steps in order to make Komodo use your private key when connecting to your server.
    1. In the Komodo Edit Preferences, choose Environment.
    2. Find the information about your SSH environment by entering the command ssh-agent in Terminal. You should see output similar to:
      SSH_AUTH_SOCK=/tmp/ssh-xxxxx/agent.xxxxx; export SSH_AUTH_SOCK;
      SSH_AGENT_PID=xxxxx; export SSH_AGENT_PID;
      echo Agent pid xxxxx;
    3. Add the following environment variables in Komodo:
      • Name: SSH_AUTH_SOCK
      • Name: SSH_AGENT_PID
      The values for these environment variables should be what you learned earlier in step 2.
    4. Press OK to save your changes.
  9. To test whether Komodo is able to successfully connect to your server, choose File -> Open -> Remote File. Select CSE 330 Cloud Instance from the drop-down menu. You should be able to see a list of files in your public_html directory.

Installing Upload Extension

Strangely, Komodo Edit does not come built-in with a mechanism to upload files from your computer to the server. Fortunately, the community has released an add-on that gives us this feature.

  1. In Komodo, go to Tools -> Addons.
  2. Search for the add-on named Uploader.
  3. Download and install it, and restart Komodo.
  4. In your Server preferences, create a new server (or rename an existing one) to be identical to your project name, but starting with a star. For example, in my project named FileShare, I would name the server *FileShare. The default path will be the location to which Komodo will upload your files. Note: The path should be absolute.
  5. You can now select a file and go to File -> Upload to upload it to your server.

Tip: To make things quicker, you can bind a keyboard shortcut like ctrl/cmd+D to the Upload feature by following these steps:

  1. In Komodo preferences, choose Editor -> Key Bindings.
  2. Find the "Upload" command under "General". Press in the "New Key Sequence" box, and press ctrl/cmd+D. Proceed through the on-screen instructions; you can name your new scheme Custom.
  3. Save the preferences and restart Komodo. You will now be able to upload files by simply pressing ctrl/cmd+D.

Starting a Project

When you start a new project, whether individual or group, you should create a new directory and a new Komodo Project file.

  1. Create a new directory in your repository named after the project you will be starting (e.g., fileshare).
  2. In Komodo, choose Project -> New Project (or press shift-ctrl-N).
  3. Navigate to the directory you just created, enter a name for the project (e.g., FileShare.komodoproject), and press "Save".
  4. You should now see a window like this:
  5. Press ctrl-N (or cmd-N) to create a new file. Save it in your project. For example, you could create a page named index.html with the Quick and Easy Page Layout:
  6. Continue creating and editing the files from your site.
    Tip: To change between files without using a mouse, press ctrl-PageUp and ctrl-PageDown (cmd instead of ctrl on OS X). Many computers without explicit PageUp and PageDown buttons bind them to fn-Up and fn-Down. For example, on a MacBook Pro, to change to the next tab, you would press three keys: fn+cmd+down.
  7. When you are ready to upload, go into Komodo Edit preferences and add a new SFTP server. Name the server *ProjectName — that is, name it the same as your project, but prepend an asterisk (*). For example, for our FileShare.komodoproject project, we would name the server *FileShare.
  8. You can now use the Upload extension you installed earlier to upload files from your working directory to your EC2 instance.