Bioinformatic Course II

#Linux Command Line For Biologists

What we will cover today

1. Bash scripting basics
2. Working through the network
3. Using ARC resources
4. Linux command recipes for bioinformatics

Using Linux: there's more than one way to get there.

1. Buy a mac and install homebrew. $$$$

2. Buy an old machine an install linux on it. $

3. Virtual Machines. Free ! sometimes laggy

   3.1 VirtualBox https://www.virtualbox.org

   • Use it in full screen.
   • Turn on 2D and 3D acceleration.
   • Install Guest Addition (already done).

   3.2 VMWare Player https://my.vmware.com/web/vmware/free#desktop_end_user_computing/vmware_player/6_0

4. SSH Clients. Free ! It's just a client

SSH Secure Shell Client https://shareware.unc.edu

Putty http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

5. Dual Boot. Free ! not simple for windows 8

Download bootable USB drive or CD image [see tutorial] (http://askubuntu.com/questions/221835/installing-ubuntu-on-a-pre-installed-windows-8-64-bit-system-uefi-supported) 6. Native Client. Windows Only, Free ! Chunky and Grumpy

Cygwin https://www.cygwin.com

see tutorial

Start to use linux today!

Know where you are and setup your working environment

Your first bash script

Get your data to and from a remote machine

Bioinformatic Recipes (Next Generation Sequencing)