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rnaseq_requirements

COMPUTER REQUIREMENTS

By using Linux on your own computer you can more quickly incorporate what you learn into your own research. Before the first class, please ensure you have done the following…

  1. Selected a computer to use in the class
  2. Downloaded required software
  3. Requested a Summit user account

1) Select a computer to bring to class

You will need to have either a MAC laptop or a laptop running Windows 10 (Anniversary Update or higher) or a Linux laptop. We will no longer be supporting PC laptops running Windows versions less than 10. If you don't have a MAC, Windows10, or Linux laptop, please obtain one. There are laptops available for rental through the Morgan Library. Your graduate program or your lab may have laptops to borrow.

The computer should be a laptop. A tablet-only or iPad is not going to cut it.


2) Download and install all required software

You will need…

  1. a text editor (see below)
  2. R and R Studio (see below)
  3. IGV (optional, see below)

text editor

Everyone will need to install a text editor for writing and modifying plain text files. We recommend BBEdit for Mac and Notepad++ for windows. We DO NOT recommend TextEdit, Wordpad, Notebook, or Microsoft Word. You are free to use vim or emacs if you are already familiar with those interfaces, but they are beyond the scope of this course.

  • Mac: we recommend BBEdit . Click Download under the BBEdit software. You don't need to buy it. The free version does everything you need.

  • We do not recommend TextEdit, Wordpad, Notebook, EMACS, or Microsoft Word.
  • If you already have a text editor you like that is not listed, you are free to use it provided it saves files in true flat .txt and not rich text format.

R and RStudio

MAC USERS

MAC: To Install R

  • Open an internet browser and go to www.r-project.org.
  • Click the “download R” link in the middle of the page under “Getting Started.”
  • Select a USA CRAN location (a mirror site) and click the corresponding link.
  • Click on the “Download R for (Mac) OS X” link at the top of the page.
  • Click on the file containing the latest version of R under “Files.”
  • Save the .pkg file, double-click it to open, and follow the installation instructions.
  • Now that R is installed, you need to download and install RStudio.

MAC: To Install RStudio

  • Click on “Download RStudio Desktop.” (the free version)
  • Click on the version recommended for your system, or the latest Mac version, save the .dmg file on your computer, double-click it to open, and then drag and drop it to your applications folder.

PC USERS

PC: To Install R:

  • Open an internet browser and go to www.r-project.org.
  • Click the “download R” link in the middle of the page under “Getting Started.”
  • Select a USA CRAN location (a mirror site) and click the corresponding link.
  • Click on the “Download R for Windows” link at the top of the page.
  • Click on the “install R for the first time” link at the top of the page.
  • Click “Download R for Windows” and save the executable file somewhere on your computer. Run the .exe file and follow the installation instructions.
  • Now that R is installed, you need to download and install RStudio.

PC: To Install RStudio

  • Click on “Download RStudio Desktop.” (the free version)
  • Click on the version recommended for your system, or the latest Windows version, and save the executable file. Run the .exe file and follow the installation instructions.

IGV: Integrative Genome Viewer (optional)

Download and install IGV. You may need to update java:


3) Request a Summit user account

Please note… if you took DSCI510 - you are already signed up!

Summit is a high performance computing cluster (a.k.a. supercomputer) that is housed at the University of Colorado Boulder and available for us to use.

Please request access to Summit by going to HPC Summit: Get Started and starting on Step 3. Here are some tips:

  • When asked what you want to use SUMMIT for, you can just say you are taking DSCI512
  • Please check the box indicating you want to use Summit.

To access SUMMIT you will need a DUO app on your phone. Many CSU students already have this, but in case you don't, go here for instructions to download: DUO

rnaseq_requirements.txt · Last modified: 2021/06/01 15:05 (external edit)