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ljmciver edited this page Jan 25, 2021 · 3 revisions

Welcome to the bioBakery Workshop!

Your instructor will provide you with the information for the current workshop:

  1. The connection method (Web Browser, VNC Viewer, or SSH)
  2. The name or IP address of your instance
  3. The password (and user name if required)

Please follow the instructions under the connection method above for your workshop to get started in bioBakery Google Cloud.

Table of contents

Option 1: Web Browser Connection

The web browser based connection will provide you with desktop access to the bioBakery Google Cloud instance. It will also provide you with a method to download and upload files to your bioBakery instance.

How to Connect

Follow the instructions below to connect to your instance through your web browser.

Step 1: Log in to the bioBakery Guacamole Server

  1. Go to the http://huttenhower.sph.harvard.edu/guacamole
  2. Login with the Guacamole username and password provided by your instructor

The Guacamole Server log in screen is shown below.

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Step 2: Connect to your instance

  • After you login, you will see the home screen.

The initial Guacamole bioBakery home screen is shown below.

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The Guacamole bioBakery home screen, after you have connected to an instance, is shown below.

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  • Double click on the name of your instance, provided by your instructor, to connect to the desktop of your instance.
  • If you see the following error, "The Guacamole server is denying access to this connection because you have exhausted the limit for simultaneous connection...", you have selected an instance that is currently being used by another student. Please select Home from the options and then connect to a different instance.

The bioBakery Google Cloud desktop through the Guacamole server is shown below.

image

File Transfer

You can download and upload files to your instance. First connect to your instance, then follow the instructions below to transfer files.

Upload Files

  • To upload files to your bioBakery instance, drag and drop the file into the desktop
  • The uploaded file will be located in your $HOME directory, which is /home/hutlab_public/
  • A file transfer status box will be displayed in the lower right-hand corner of the screen

The file transfer status box is shown below.

image

  • An alternative to the drag and drop method is to upload the files from the menu
  • To upload the files from the menu follow these steps
  1. Type Ctrl+Alt+Shift to bring up the menu on the right side of the page
  2. In the menu, click on the box under Devices

The menu is shown below.

image

  1. Click on the Upload Files button on the upper right-hand side of the menu
  2. Select the file to upload and click Open
  3. A file transfer status box will be displayed in the lower right-hand corner of the screen
  4. The uploaded file will be located in your $HOME directory, /home/hutlab_public/
  5. Type Ctrl+Alt+Shift to close the menu on the right side of the page and return to your desktop

Download Files

  1. Type Ctrl+Alt+Shift to bring up the menu on the right side of the page
  2. In the menu, click on the box under Devices

The menu is shown below.

image

  1. A new menu will appear, listing the root folders on your instance

The menu of root folders is shown below.

image

  1. In the menu, double click on the folders to get to the folder containing the file(s) on your instance you would like to download

The menu of the $HOME folder, /home/hutlab_public/, is shown below.

image

  1. In the menu, double click on the file(s) you would like to download
  2. A file transfer status box will appear in the lower right-hand corner listing the files you selected to download
  3. Click on the links in the file transfer status box to download the files to the Downloads folder on your computer

The file transfer status box with download links is shown below.

image

  1. Type Ctrl+Alt+Shift to close the menu on the right side of the page and return to your desktop

Clipboard

To copy text from your bioBakery instance to your computer, first highlight and right-click to copy the text to the instance clipboard. Then bring up the menu by typing Ctrl+Alt+Shift and see the text you copied in the first box. Now this text is available for you to copy to any other location on your computer.

To copy text from your computer to your bioBakery instance, first highlight and right-click to copy the text to your computer clipboard. Then bring up the menu in your instance by typing Ctrl+Alt+Shift and now paste the text into the first box. Now this text is available for you to copy to any other location on your instance.

The menu with the clipboard section is shown below:

image

Please note, if you experience issues with copying to the clipboard and pasting in the terminal, please close the terminal and reopen. This action will synchronize the terminal clipboards and allow you to copy and paste again.

How to Disconnect

To disconnect from your instance, type Ctrl+Alt+Shift to bring up the menu on the right side of the page. From the drop down under your user name, select X Disconnect.

If you type Ctrl+Alt+Shift and you do not see a menu, click on the page to activate that screen, then try Ctrl+Alt+Shift again.

The menu with the drop down selection is shown below.

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To log out of the Guacamole server, click on the menu on the top right-hand side of the home page and select Logout.

The Guacamole home page menu is shown below.

image

Option 2: VNC Viewer Connection

The VNC Viewer connection will provide you with desktop access to the bioBakery Google Cloud instance.

How to Connect

Follow the instructions below to connect to your instance through VNC Viewer.

Step 1: Install a VNC Viewer

  • We suggest Real VNC Viewer which is available for all platforms.
  • We suggest installing the Real VNC Viewer Google Chrome App as this install is platform independent.
  • If instead you would like to install Real VNC Viewer, you only need to download Real VNC Viewer for your platform and it should be ready to run.

Step 2: Start a VNC Viewer

  • If you installed Real VNC Viewer, just launch the Chrome App (or run the download) to start it.
  • The login screen for Real VNC Viewer is shown below.

image

Step 3: Connect to the instance

Type in the following information into the prompts in the VNC Viewer:

  • Address : IP_ADDRESS:5901
    • Replace IP_ADDRESS with the IP address of your instance, the IP address will be provided by your instructor
    • For example, in the address box you might provide 123.168.100.200:5901
  • Password : the password will be provided by your instructor

During the login, with Real VNC Viewer (the free version) you will see a message about encryption, click accept as it is okay that the connection is not encrypted (though the password will be encrypted).

The bioBakery Google Cloud desktop is shown below.

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How to Disconnect

To disconnect from your VNC Viewer connection, click the X in the menu on the bottom of the screen (if running Real VNC Viewer, Google Chrome App).

The Real VNC Viewer, Google Chrome App, menu is shown below.

image

Option 3: SSH Connection

The SSH connection will provide you with a terminal and command prompt to access the bioBakery Google Cloud instance.

How to Connect

Follow the instructions below to connect to your instance with SSH.

Step 1: Login to the Google Cloud Console

  1. Go to the Google Cloud Console: http://console.cloud.google.com
  2. Login with the google username and password provided by your instructor a. If you are not prompted to login, please log out of your personal google account and try the link again

Step 2: Start an SSH connection

  1. Click on the three bars on the upper left-hand corner of the page to bring up a menu
  2. In the menu, click on Compute Engine then VM instances
  3. Identify your instance, the name provided to you by your instructor, from the list in the center of the page
  4. Click on the SSH in the same row as your instance name to connect

The Google Cloud Compute Engine/VM instances list with the SSH connect button is shown below.

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The Google Cloud SSH terminal is shown below.

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How to Disconnect

To disconnect from your SSH connection, type exit at the command prompt.

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