ngs bioinformatics workshop 1.1 tutorial – preparing for bioinformatics work march 8 th, 2012...

NGS Bioinformatics Workshop1.1 Tutorial – Preparing for Bioinformatics Work

March 8th, 2012IRMACS, SFU

Facilitator: Richard BruskiewichAdjunct Professor, MBB

Learning Objectives

Using the Cloud as a (“free”) sandboxGetting Started – logging into resources (ssh)Basic LinuxPrimer on installing software (useful elsewhere)

Getting Started – WestgridQuick tour…

Introduction to Galaxy:@ the movies…

Disclaimer… If you don’t want to mess up your home computer with a

second guest operating system but want to try new things out, playing in a sandbox “in the cloud” may be cost effective.

You can surf for “cloud” vendors available (Amazon, Microsoft Azure, Google Apps, RackSpace, Salesforce.com, IBM, etc.)

You can often avail of their “free” allotments(?). They are (relatively) easy to experiment with and relatively cheap (for small experiments).

I don’t work for Amazon nor have any financial interest, but this demo will use Amazon (probably the largest and most established (since 2006) cloud vendor) because I know it well enough to be a good tour guide.

Playing on the Cloud (aws.amazon.com)

http://aws.amazon.com Documentation

http://docs.amazonwebservices.com/AWSEC2/latest/GettingStartedGuide/Welcome.html?r=5350

Accessing cloud on the web: https://console.aws.amazon.com

SSH access to remote serversssh on Unix/Linux/OSX (putty on Windows)

Linux PrimerBasic Unix command line (basic shell, man)

http://vic.gedris.org/Manual-ShellIntro/1.2/ShellIntro.pdf

Upgrading your Linux (Unix) OS: yum / apt-get (Synaptic); OSX equivalents

(DMG?)Basic computer language support:

gcc, Perl, Python (Active* for Windows)

Installing Other (Linux) Software Installing other basic software

Download software…check yum/apt-get first…Checking file integrity with md5sum, sha1, etc.

opensslUnpacking:

gunzip/tar, tar zxvf, bunzip2, unzip(Linux) file permissions – common source of problemsLook for README & INSTALL

Precompiled binaries(?)Configure; installing pre-requisites (e.g. gcc)perl modulespython modulesR modules

Deployment: root privileges & sudo

Getting Started - Westgrid

http://www.westgrid.ca/support/quickstart/new_users http://www.westgrid.ca/support/software#bioinformatics

Bugaboo @ SFU has several packages already including ABySS

Breezy @ U Calgary has ALLPATHS-LG, Picard, SOAPdenovo, Velvet, wgsim (!)

Logging into resourceshttp://www.westgrid.ca/support/quickstart/bugaboo

Galaxy Genomics Workbench

http://galaxy.psu.edu/