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NGS Bioinformatics Workshop
1.1 Tutorial – Preparing for Bioinformatics Work
March 8th, 2012
IRMACS, SFU
Facilitator: Richard Bruskiewich
Adjunct Professor, MBB
Learning Objectives
Using the Cloud as a (“free”) sandbox
Getting Started – logging into resources (ssh)
Basic Linux
Primer on installing software (useful elsewhere)
Getting Started – Westgrid
Quick 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/lat
est/GettingStartedGuide/Welcome.html?r=5350
Accessing cloud on the web:
https://console.aws.amazon.com
SSH access to remote servers
ssh on Unix/Linux/OSX (putty on Windows)
Linux Primer
Basic Unix command line (basic shell, man)
http://vic.gedris.org/ManualShellIntro/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.
openssl
Unpacking:
gunzip/tar, tar zxvf, bunzip2, unzip
(Linux) file permissions – common source of problems
Look for README & INSTALL
Precompiled binaries(?)
Configure; installing pre-requisites (e.g. gcc)
perl modules
python modules
R 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 resources
http://www.westgrid.ca/support/quickstart/bugaboo
Galaxy Genomics Workbench
http://galaxy.psu.edu/