Software Requirements & Setup Instructions

To fully participate in this boot camp, you will need access to the software described below on your own laptop (N.B. You will likely need Administer privileges/permissions to install some of these).


Request your account at GreatLakes cluster for Day 4

First, you will need to apply for GreatLakes cluster account for Day 4 by following the steps below.

  • Visit https://arc-ts.umich.edu/greatlakes/user-guide/ with your laptop.
  • Under the #2 at the top of the page, click on the Fill Out Form button.
  • Login using your Kerberos password and Duo two-factor authentication.
    • If you have not activatived duo two-factor authentication yet, please visit UMICH Duo Page to get one.
  • Enter hmkang (Hyun Min Kang) as advisor’s name.
  • Enter hmkang@umich.edu as advisor’s email.
  • For “college or department” have them select: Medicine
    • It is very important to select Medicine, NOT your own school or department for this purpose of bootcamp.
  • For “describe project” put: bioinformatics bootcamp
  • For “ARC-TS services” select: Great Lakes
  • Tick I agree and click Submit button to complete your request.
  • Mark in the attendance sheet that you have completed the request so that instructors can double check later.


The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows: Install MobaXterm, an enhanced terminal with bash for Windows. Note that the default ‘Personal Edition install’ typically places the MobaXterm executable in C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition.

Please also install the Plugin CygUtils. Once downloaded please move the CygUtils.plugin file to the folder C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition. Launching mobaxterm will complete the install.

Mac OS X: You do not need to install anything. You can access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this class.

Linux: There is no need to install anything.


Git

Git is a version control system that lets you track who made changes to what and when. To work with GitHub and BitBucket you will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows: Git should be installed as a plugin to mobaxterm. Download the plugin for Git. Once downloaded please move the Git.mxt3 file to the folder C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition. Launching mobaxterm will complete the install.

Mac OS X: For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labeled “snow-leopard” available here.

Linux: If Git is not already available on your machine you can install it via your distro’s package manager. For Debian/Ubuntu run

sudo apt-get install git

and for Fedora run

sudo yum install git.


Text Editor

When you’re writing code, it’s nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case ‘q’, exclamation mark), then hitting Return to return to the shell.

Windows: nano is a basic editor and the default that instructors use in the workshop. Nano should be installed as a plugin to mobaxterm (see above Git instructions for windows).

Mac OS X: nano should be pre-installed.

Linux: nano should be pre-installed.


R and RStudio

R Binaries for Windows, MacOSX and Linux can be downloaded and installed from CRAN (Comprehensive R Archive Network). If possible download the latest binary version of R for your operating system. As of course launch (Aug 16) the latest release (2019/08/21, “Action of the Toes”) is R-3.6.1.

After installing R itself we recommend installing RStudio desktop (v1.2.1335 or above), a slick visual interface for R.


Python

Python is a popular language for scientific computing. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.6 or later.

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows: Download and install Anaconda. Download the default Python 3 graphical installer installer. Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X: Download and install Anaconda. Download the default “Mac OS X Python 3.7 Graphical Installer”. Use all of the defaults for installation.

Linux: As above, we recommend the all-in-one scientific Python installer for linux Anaconda.