2021-04-26-umich-rnaseqDemystified

Setup instructions

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

• A Macintosh or Windows workstation connected to the internet.
• Administrative privileges on this workstation.
• About 30 minutes (~20 minutes unattended).

Table of Contents

• Introduction
  • How to get help
• Windows setup
  • Zoom
  • Git-Bash
  • Installing R/RStudio
  • Notes
• Macintosh setup
  • Zoom
  • Terminal
  • Installing R/RStudio
  • Notes

Introduction

• The workshop will be conducted over Zoom, Linux (first day), and R with RStudio (second day).

  • The workshop exercises are designed to work well for Windows or Mac users and the installation instructions are detailed in separate sections below.

  • If you do not have Administrative privileges it will be tricky to install R/RStudio; you may need to coordinate with your System Admin/IT Support team to get these installed. See How to get help below if you need more guidance on this.

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).
  • Whether you have Administrative privileges on your workstation.
  • The specific text of any error messages, if applicable.

Windows setup

Zoom

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

Windows PowerShell / git-bash

Git-bash and Windows Subsystem for Linux (WSL) are programs that enable you to connect to our workshop Linux environment. WSL is a powerful option, but can be difficult to install/configure. If you have WSL installed and you are comfortable using it, you can use that and skip to the next section.

1. To download git-bash, in a web browser, go to: https://git-scm.com/downloads and click on Windows. Save and open the executable file to launch the installer.

2. The git-bash installer presents many options; repeatedly click Next to simply accept all the default options. At the end of this series of questions, you can click Install.

3. The installer will show a progress bar; this should take less than a minute. Note: you may see a warning towards the end "Unable to run post-install scripts; no output?"; this will not impact your installation and you can ignore it by clicking Ok.

4. On the final screen (Completing the Git Setup Wizard) you can uncheck View Release Notes option and click Finish. The installer will close.

5. To launch git-bash, from Start Menu, select "Git Bash"; this will create a new window with a command prompt that looks something like this:

• your_username@WSRTS001 MINGW64 ~ $

If you can't install or launch git-bash, or if it returns an unexpected result, please see How to get help for more assistance.

Installing R/RStudio (Windows)

1. RStudio depends on the R programming environment, so we have to install that first. In a web browser, open: https://cran.rstudio.com/bin/windows/base/ and click "Download R 4.0.3 for Windows" (the version may be slightly different). Open the downloaded executable to launch the R installer.

2. The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes about 2 minutes; click Finish when prompted to close the installer.

3. To install RStudio, in a web-browser, open: https://rstudio.com/products/rstudio/download/#download and click on Download RStudio Desktop for Windows. Open the downloaded executable to launch the installer.

4. The installer will either prompt you to login as an Admin user or (if your current account has Admin privileges) simply ask you to allow it to make changes. Click Yes

5. The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes less than one minute; click Finish when prompted to close the installer.

6. Press Windows+R keys to open the Run dialog; type "RStudio" in the text box and hit enter. This will launch a new RStudio window. The RStudio window is divided into several panes. The lower left pane shows the Console tab and will show some text followed by a command prompt (>):

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

7. The workshop exercises requires the installation of special R libraries. To install them into RStudio, copy the block of text below, paste into the RStudio Console tab, and press Enter to execute. (Note: These installations automatically trigger the installation of a litany of dependent libraries so you will see repeated progress bars and code flying by in the Console window. This step takes about 15 minutes, so now is a good time to get coffee/tea while RStudio cooks.)

install.packages("tidyr")
install.packages("ggplot2")
install.packages("pheatmap")
install.packages("ggrepel")
install.packages("formattable")
install.packages("RColorBrewer")
install.packages("matrixStats")
install.packages("dplyr")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt", ask=FALSE)
BiocManager::install("DESeq2", ask=FALSE)
missing <- setdiff(c("tidyr", "ggplot2", "pheatmap", "ggrepel", "formattable", "RColorBrewer", "matrixStats", "dplyr", "biomaRt", "DESeq2"), rownames(installed.packages()))
if (!length(missing)) { cat("Ready for Computational Foundations workshop\n")} else {cat("PROBLEM: could not install:", missing, "\n")}

8. The Console output should conclude with the text:
   Ready for Computational Foundations workshop.

9. Press Control-Q close RStudio; when prompted to Save workspace image..., click Don't Save.

If you had problems installing R/RStudio or installing the R libraries above, please see the How to get help section above for more assistance.

Your Windows workstation is ready for the workshop. Thank you for your patience and fortitude.

Notes (Windows)

• Following the workshop, you can remove any of Git-bash, R and RStudio. As an Admin user, go Start > Settings > Apps & Features. Click on the program to remove and click Uninstall.

Macintosh setup

Zoom

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

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

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

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

   1. System Preferences >> Security & Privacy: click on the Privacy tab
   2. Select Accessibility on left tab
   3. Scroll to the bottom on the right tab and verify Zoom is checked.
   4. 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.
   5. Click the lock again.
   6. Close and relaunch Zoom client.

Terminal

1. Macintosh 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: Thu Dec 10 12:44:03 on ttys003
MacBook: ~ your_username$

2. At the command prompt, type date and press Return. The Terminal should print the current date and time.

Installing R/RStudio (Macintosh)

1. RStudio depends on the R programming environment, so we have to install that first. In a web browser, open:

• https://cran.rstudio.com/bin/macosx/

  and click the link "R-4.0.3.pkg" (the version may be slightly different). Open the downloaded executable to launch the R installer.

2. The installer will walk through several options; accept all the defaults (by repeatedly clicking Continue) and when prompted, click Install. The installer will prompt you to confirm your username/password. The installer will show a progress bar; the process takes about 1 minutes; click Finish when prompted to close the installer.

3. To install RStudio, in a web-browser, open:

• https://rstudio.com/products/rstudio/download/#download and click on Download RStudio Desktop for Mac.

4. Opening the downloaded executable opens a window with "RStudio" and your Applications folder icons. Drag the RStudio into the Applications folder. (If you see a dialog that claims RStudio already exists, click Keep Both.) The installer will prompt you to confirm your username/password.

5. The installer will walk through several options; accept all the defaults (by repeatedly clicking Next) and when prompted, click Install. The installer will show a progress bar; the process takes less than one minute.

6. When completed, open the Applications folder and double-click on the RStudio application. You will see a dialog "RStudio.app is an app downloaded from Internet. Are you sure you want to open it?" Click Open. This will launch a new RStudio window. The RStudio window is divided into several panes. The lower left pane shows the Console tab and will show some text followed by a command prompt (>):

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

7. The workshop exercises require the installation of special R libraries. To install them into RStudio, copy the block of text below, paste into the RStudio Console tab, and press Enter to execute. (Note: These installations automatically trigger the installation of a litany of dependent libraries so you may see repeated progress bars and lots of code flying by in the Console window. This step takes about 15 minutes, so now is a good time to get coffee/tea while RStudio cooks.)

install.packages("tidyr")
install.packages("ggplot2")
install.packages("pheatmap")
install.packages("ggrepel")
install.packages("formattable")
install.packages("RColorBrewer")
install.packages("matrixStats")
install.packages("dplyr")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("biomaRt","DESeq2"), update=FALSE, ask=FALSE)
missing <- setdiff(c("tidyr", "ggplot2", "pheatmap", "ggrepel", "formattable", "RColorBrewer", "matrixStats", "dplyr", "biomaRt", "DESeq2"), rownames(installed.packages()))
if (!length(missing)) { cat("Ready for Computational Foundations workshop\n")} else {cat("PROBLEM: could not install:", missing, "\n")}

8. The Console output should conclude with the text Ready for Computational Foundations workshop

9. Press Command-Q close RStudio; when prompted to Save workspace image..., click Don't Save.

If you had problems installing R/RStudio or installing the R libraries above, please see the How to get help section above for more assistance.

Your Macintosh workstation is ready for the workshop. Thank you for your patience and fortitude.

Notes (Macintosh)

• Following the workshop, you can remove any of R and RStudio. Open your Applications directory, and drag the R or RStudio application into the Trash.