This document guides you through the preliminary steps necessary to participate in the workshop. To complete this setup, you will need:

  • A Macintosh or Windows workstation connected to the internet.
  • An email invitation to the workshop Slack workspace.
  • A UM uniqname and password.
  • A Duo app on your smartphone or tablet.
  • About 10 minutes.

Introduction

  • The virtual workshop will be conducted using Zoom and Slack for all days.
  • Attendees will use their own workstation/laptop to participate; the workstation/laptop should have a microphone, camera, and reliable internet access. While not required, for laptop users we recommend using a larger monitor for the optimal workshop experience.
  • The workshop will use Slack for group messaging. Messages posted to the general channel will be visible to all participants in the workshop.
  • We will be using compute and storage provided by UM Advanced Research Computing. All required software and data will be pre-installed in a workshop account.

How to get help

While we have endeavored to make this setup process work robust and comprehensive, installing bioinformatics software is tricky and we would be happy to lend a hand to get things working.

  • If you have problems/questions, please don’t hesitate to email us at: bioinformatics-workshops@umich.edu

  • When emailing it will speed things along if you could include:

    • Whether you are using Windows or Mac (and optionally which version of the OS you are using).
    • The specific text of any error messages, if applicable.

Setup steps

1. Zoom

If you have not used Zoom before, please use the following link to install “Zoom client for Meetings”
https://zoom.us/download

  • Additional Zoom settings for Macintosh:

    1.1 To enable screen sharing (useful for breakout rooms and tech support)

    • System Preferences >> Security & Privacy: click on the Privacy tab
    • Select Screen Recording on left tab
    • Scroll to the bottom of the right tab and verify Zoom is checked.

    1.2. To enable remote control (useful for breakout rooms and tech support)

    • System Preferences >> Security & Privacy: click on the Privacy tab
    • Select Accessibility on left tab
    • Scroll to the bottom on the right tab and verify Zoom is checked.
    • If it’s not checked, click the lower left lock icon and enter user password when prompted. You can now check Zoom in the right tab.
    • Click the lock again.

    1.3. Close and relaunch Zoom client.

2. Slack

2.1. In the Slack email invitation from the hosts, click the link to join the Slack workspace.

2.2. Follow the Slack instructions to login or create an account. You may edit your profile to add a photo if you choose.

2.3. Note that once your Slack account is established and you have accepted the Slack invite you can access the Slack channel by pointing your web browser here:
https://umbioinfcoreworkshops.slack.com

3. Install Duo 2-Factor Authentication (2FA)

Duo 2FA ensures access to computing resources are secure. You can skip this step if you already have Duo installed on your smartphone or tablet.

3.1 Follow the instructions under “Get Started Now”:
https://safecomputing.umich.edu/two-factor-authentication/turn-on-weblogin

4. Establish a Great Lakes user login

If you already have an active Great Lakes user login you can skip to step 5 below. (And if you are not sure whether you have a login, you can try step 5 below and come back here if your login fails.)
ARC staff typically process these requests very quickly, but it would be diligent to submit this request ASAP.

4.1 In your browser, go to:
https://arc-ts.umich.edu/login-request
You may be prompted to login using your uniqname, level-1 password, and Duo 2FA.

4.2 In the form, enter the following information:

  • Advisor’s Name: Chris Gates
  • Advisor’s Email:
  • College or Department: Medicine
  • Please describe projects…: BioinfCore Reproducible Computing Workshop
  • The ARC services need…: Great Lakes
  • Your screen will look something like this:
    Request Great Lakes user login

4.3 Review and accept the terms of service and submit the request.

You will need to pause here until you receive an email from ARC confirming that your account has been created.

5. Login to the shared server from your web browser

5.1. In your web browser, follow this link:
https://greatlakes.arc-ts.umich.edu/pun/sys/shell/ssh/greatlakes.arc-ts.umich.edu

5.2 The first time you do this, you may see a standard UM Weblogin page (below). Enter your uniqname and level-1 password and click Log-In. Check your phone/tablet for a Duo 2FA Push notice and Accept.
UM Weblogin

5.3 Your browser will update to show a terminal window with a banner showing brief terms of use followed by a password challenge (below). Click in this window to ensure the browser has focus and type your level-1 password followed by the Enter or Return key.
PLEASE NOTE: the password prompt does not change as you type your password - while unsettling, this is ok and it is actually accepting your password. OOD Password Challenge

5.4 The terminal window inside the browser will prompt for Duo authentication; choose a method and accept the Duo challenge on your phone or tablet. OOD 2FA Challenge

5.5 The terminal window will update to show welcome text and a command prompt. Note that you may see some red text warning about ARC Maintenance and your prompt may look slightly different than below; that’s ok. gl-login-node

5.6 At the command prompt copy & paste the following command followed by Enter/Return key
/nfs/turbo/umms-bioinf-wkshp/workshop/bin/setup-complete

The command should show a block of text like this:

Thank you for taking the time to setup and test your configution
in advance of the workshop. We look forward to seeing you soon!

If you see the text above, you have successfully logged into Great Lakes and you are ready for the workshop.

You can close this window by typing exit at the command prompt or simply closing the browser window.

Congratulations

Your workstation and logins are ready for the workshop; thank you for taking time to set this up in advance.

  • You can close the terminal window by typing exit or simply closing the browser tab.

Launch a command window via SSH

  • If you are using Windows:

    • Press Windows Key + R to launch a command window. Make sure the Open field says cmd and click OK.

    • You will see a new command window containing something like this (yours may have more text and the last line may look a bit different; that’s ok)

      Microsoft Windows [Version 10.0.17763.1935]
(c) 2018 Microsoft Corporation. All rights reserved.

H:\>

  • If you are using a Mac:

    • Macintosh OSX has a built in command window called Terminal. Press Command + Space to launch Spotlight. In the search field, type “Terminal” and double-click on the top result.

    • You will see a new Terminal window containing something like this (your may have more text and the last line may look a bit different; that’s ok)

      Last login: Feb 10 12:44:03 on ttys003\
MacBook: \~ your_username\$

Login to Great Lakes

  1. In the command window, type the following command, replacing the YOUR_UNIQNAME with the username supplied to you by the workshop hosts; hit Enter or Return to execute the command.
    Note: you can copy the command below to the clipboard and then right-click in the command window to paste.

    ssh

  2. The first time you run this command, you may see a prompt like the following; type yes and hit Enter/Return to continue.

    The authenticity of host ‘…’ can’t be established. ECDSA key fingerprint is SHA256:nz9lJaGEI5QFy7…. Are you sure you want to continue connecting (yes/no/[fingerprint])? yes

The command will print a warning (e.g. Warning: Permanently added ‘SERVER_ADDRESS’ (ECDSA) to the list of known hosts). This is fine.

  1. Your browser will update to show a terminal window with a banner showing brief terms of use followed by a password challenge (below). Type your level-1 password followed by the Enter or Return key.
    PLEASE NOTE: the password prompt does not change as you type your password - while unsettling, this is ok and it is actually accepting your password. OOD Password Challenge

  2. If you typed your password correctly, you will see a prompt for Duo authentication; choose a method and accept the Duo challenge on your phone or tablet. OOD 2FA Challenge

  3. The terminal window will update to show welcome text and a command prompt. Note that your prompt may look slightly different than below; that’s ok.

*                      Advanced Research Computing                           *
                         University of Michigan
                         arc-support@umich.edu

                         Welcome to Great Lakes

User Guide: http://arc.umich.edu/greatlakes/user-guide/
The login nodes are for interacting with the Slurm 
scheduler or code and data management; they are not for running
workloads.  Users are limited to 2 cores and 4G of memory of memory 
for sessions on the login nodes. For more information, see the User Guide.

The folders under /scratch are intended for data that is in active
use only.  Please do not store data there for longer than 60 days.
For usage information, policies, and updates, please see:
https://arc.umich.edu/document/greatlakes-policies/
------------------------------------------------------------------------


$

A note on the shared compute environment

Please note that this workshop environment is optimized for the exercises in this particular workshop but is likely unsuitable for analyzing your own datasets. In particular: - It is not sized for compute intensive operations or large storage. - It is not secured for sensitive data of any kind. - Your access to the workshop ARC account is temporary and will be removed shortly after the conclusion of the workshop.

If you had problems or questions about the installation steps please see the How to get help section above for more assistance.