This document guides you through the installation of software necessary to participate in the computational foundations workshop. To complete this setup, you will need:
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.
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:
If you have not used Zoom before, please use the following link to
install “Zoom client for Meetings”
https://zoom.us/download
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.
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.
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.
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.
On the final screen (Completing the Git Setup Wizard) you can uncheck View Release Notes option and click Finish. The installer will close.
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:
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.
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.
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.
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.
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
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.
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.
>
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")}
The Console output should conclude with the text:
Ready for Computational Foundations workshop.
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.
If you have not used Zoom before, please use the following link to install “Zoom client for Meetings” https://zoom.us/download
To enable screen sharing (useful for breakout rooms and tech support)
To enable remote control (useful for breakout rooms and tech support)
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$
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.
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.
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.
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.
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.
>
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")}
The Console output should conclude with the text Ready for Computational Foundations workshop
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.