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      Bioinformatics: Command Line/R Prerequisites 2020

Home
Introduction
Intro to the Workshop and Core
Schedule
Resources
Zoom help
Slack help
Software and Links
Cheat Sheets
Intro CLI
Logging in
Introduction to the Command Line part 1
Introduction to the Command Line part 2
The cluster and modules
Introduction to Python
Python Part1, Background
Python Part2, Data Types
Python Part2, Solutions
Python Part3, Flow Control
Python Part3, Solutions
Python Part4, Working with Files
Python Part4, Solutions
Advanced CLI
Advanced Command Line
Advanced Challenge Solutions
A Simple Bioinformatics Workflow
Software Installation
Using make and cmake
Using Conda
Getting set up with AWS
AWS Event Engine
Starting and Stopping your AWS Instance
Introduction to R
Introduction to R
Introduction to tidyverse
Organizing, manipulating, and visualizing data in the tidyverse
Advanced R
Linear models in R
ETC
Closing thoughts
Github page
Biocore website

Logging In & Transferring Files

You should already have an account on our systems

For Macs/Linux - Logging In

  1. Open a Terminal (usually under Applications/Utilities on a Mac), or install iterm2
  2. Cut and paste this into the terminal:

    ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

  1. Type in your password. No characters will display when you are typing. Press Enter.

For Macs/Linux - Transferring files

  1. Use scp (secure copy, a remote file copying program):

    scp username@tadpole.genomecenter.ucdavis.edu:full/path/to/file .

  2. Replace ‘username’ with your username and replace ‘full/path/to/file’ with the full path to the file you want to transfer. Note that there is a “.” at the end of the command, which is where to put the file, i.e. your current directory. You will have to type in your password.

For Windows - Logging In

Windows needs a terminal to connect with, you have a few options:

  1. Shell for Windows 10
  2. Enable SSH OR
  3. MobaXterm
  4. PuTTY

In putty, mobaxterm:

  1. Open up terminal.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Make sure the Connection Type is SSH.
  4. Press “Open”. It will ask you for your username and password.

In Shell with SSH enabled:

ssh username@tadpole.genomecenter.ucdavis.edu

where ‘username’ is replaced with your username. Press Enter.

To copy / paste in Shell for Windows 10, you may need to enable keyboard shortcuts.

For Windows - Transferring files

  1. Open up WinSCP. If you haven’t installed it, get WinSCP here.
  2. In the Host Name field, type tadpole.genomecenter.ucdavis.edu
  3. Type in your username and password.
  4. Make sure the File Protocol is SFTP.
  5. Press “Login”.