1. National Center for Genome Analysis Support
Introduction to genomics software use on high performance computing systems
Le-Shin Wu, Ph.D.
Carrie Ganote
National Center for Genome Analysis Support
Genomics in July, July 22 , 2014

2. Summary High Performance Computing (HPC) cyberinfrastructure at IU
Running Applications in Command Line Interface (CLI)
Running Applications Through Graphical User Interface (GUI)
Examples

3. Who is NCGAS? Funded by National Science Foundation
Partner with TACC, SDSC, PSC, Broad
Access to High Performance Computing Systems
Bioinformatics consulting for biologists
Install and upgrade bioinformatics software
Optimized software for better efficiency
Open for business at:
Before I jump into the real technical stuff I would like to spend several minutes to talk about who we are and what we do
NCGAS is an NSF-funder organization based at IU since 2011
We partner with TACC, SDSC, PSC and broad institute
We provide computing infrastructures and bioinformatics consulting support to biologists
We also optimized bioinformatics software for better efficiency

4. HPC Cyberinfrastructure at IU
Mason large memory cluster (512 GB/node)
Quarry cluster (16 GB/node)
BigRed2 petaFLOPS cluster
Hi Performance File System DC2 (3.5 PB at 40 Gbps throughput)
Research File System (RFS) for data storage
Research Database Cluster for structured data
High Performance Storage System HPSS (15PB Type TB Disk)
High speed internal network (56 Gbps)

5. High Performance Computing System
High Performances Storage System
High Performances File System

6. Running Applications in CLI

7. System Access Use a SSH2 client to connect to the login nodes iterm
putty
ssh –Y

8. Basic linux shell commands
cd - change directories
mkdir - make directories
mv- change the name of a directory
pwd - print working directory
ls - listing of directory contents
cp - copy files
rm - remove files
cat - show file contents
less – similar to cat with backward and forward

9. Linux File System “.” current directory “..” parent directory
/home/jono/photos
(Absolute Path)
../photos
(Relative Path)

10. Running applications in command line
Know what the program is called
Bowtie, Bwa, Blast, Trinity, …
Know what programming language will be used
Java, perl, python, php, …
Prepare the inputs
Create working directory
Upload the data
Pre-processing

11. Running applications in command line
Set the commands
$>System_options Languare_options Application_name Application_options
System_options: screen, nohup, nice, time,…
Language_options: java, perl, python, php,…
Application_name: Trinity.pl, bowtie2, bwa, blastn,…
Application_options: -num_threads, -in, -out,..
$>time java -Xmx4g -Xms4g -jar /N/soft/mason/picard-tools-1.52/MarkDuplicates.jar INPUT=$SORTED_BAM OUTPUT=$MARKDUPLICATES METRICS_FILE=$METRICS REMOVE_DUPLICATES=true

12. Examples

13. Running Applications in GUI

14. What is Galaxy Galaxy is a web-based platform for analyzing data
It provides a set of tools that one can apply to the data
It stores all the activities of analyses
It allows for sharing of data sets, methods, and workflows

15. GALAXY.IU.EDU Model Quarry Mason Virtual box hosting Galaxy.IU.edu
The host for each tool is configured to meet IU needs
Quarry
Mason
Data Capacitor 2

16. Focus pane – shows options, parameters, and output for current item.
Galaxy at IU
History – shows steps previously taken to manipulate input data sets
Tool bar - contains the available steps to apply to data
What is it? -> go over user interface. Where? Diff between local and remote.
Focus pane – shows options, parameters, and output for current item.

17. Examples

18. CLI V.S. GUI Command Line Interface (CLI) Fully control
Fast and Efficient
More skills
Graphical User Interface (GUI)
Easy and User Friendly
Less skills
Black Box

19. Thank You
Le-Shin Wu Carrie Ganote NCGAS