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rnaseq_requirements

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COMPUTER REQUIREMENTS

Please bring a laptop computer to class. By using Linux on your own computer you can more quickly incorporate what you learn into your own research. Before the first class, please…

  1. Select a computer to bring to class
  2. Request a Summit user account
  3. Download and install all required software

1) Select a computer to bring to class

You will need to bring 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 contact Erin Nishimura. We have Mac OS laptops you can borrow for part or all of the course, available for use during the class time. You will still need to make your own arrangements to perform Assignments outside of class in some other way.

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


2) Request a Summit user account

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 starting on Step 3 under HPC Summit: Get Started.

To do Step 3 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


3) Download and install all required software

You will need…

  1. an ssh Client. MAC people can just use their terminal. Windows users should have puTTy or some similar ssh client.
  2. a text editor
  3. an ftp client
  4. R and R Studio

ssh client

MAC people: you are all good. Nothing to download. You can use the terminal.

PC people: Please download and install PuTTy PuTTy


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.


ftp client

We will use an interactive ftp client to transfer and edit files on remote servers. We recommend Cyberduck . Cyberduck is available on MacOS and PC. The Cyberduck in the Apple Store costs money, and we don't recommend it. Just obtain the free version from the cyberduck website.


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

  • Go to www.rstudio.com and click on the “Download RStudio” button.
  • Click on “Download RStudio Desktop.”
  • 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

  • Go to www.rstudio.com and click on the “Download RStudio” button.
  • Click on “Download RStudio Desktop.”
  • 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

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

rnaseq_requirements.1543323589.txt.gz · Last modified: 2018/11/27 05:59 by erin