Oct 8, 2012
Location: ACES 2.402 ; 9 am - 2 pm (CDT)
Your Instructors
Name |
Initials |
Affiliation |
Expertise |
|---|---|---|---|
Matt Vaughn |
MWV |
Manager, TACC Life Sciences |
|
John Fonner |
JF |
Research Associate, TACC Life Sciences |
|
Outline
Linux and Lonestar Refresher Course (9:00-10:00)
- Introduction to TACC DONE
- Linux basics with Lonestar DONE
- Logging in via SSH
- Command-line tricks (tab completion and the history)
- Essential Linux commands
- Wildcards and special file names
- Using options with Linux commands
- Getting help
- Lonestar Essentials
- The login (or head) nodes
- Acceptable uses for login nodes
- What not to use login nodes for
- Lonestar file systems
- Methods for running computing jobs
- Batch
- Interactive
- The login (or head) nodes
- How to edit files
- Using nano on the command line
- Using TextWrangler, Notepad++, or gEdit from a desktop environment
- Finding and using software
- Linux PATHs DONE
- The modules system DONE
- avail, list, load, swap, unload, key
- Extra: List of modules available at TACC
- Extra: Installing your own Linux software
Break (10:00-10:15)
Delving into HPC-oriented NGS analysis (10:15-11:15)
- Presentation: Survey of the NGS analytical landscape
- Tutorial: Read mapping with BWA and BOWTIE DONE
Speeding up your analyses using parallel computing (11:15-11:50)
- Introduction: Parallelism Strategies (PDF) DONE
- Tutorial: Using threads to speed up mapping on a single compute node DONE
- Tutorial: Using the TACC Parametric Launcher to speed up mapping (or any other natively parallel task) across multiple nodes DONE
- Bonus example: Using the Launcher to automate Rscript analyses DONE
Set-up for Afternoon (11:50-12:00)
- Pre-flight instructions for Interactive Computing session (please complete before going to lunch) DONE
Lunch (12:00-1:00)
- Please return promptly!
Variant Calling with SAMtools (1:00-1:40)
- Tutorial: Variant calling using SAMtools DONE
- Calling SNPs and Indels
- Inspecting alignments supporting a variant using tview
- Filtering variants
- Finding summary statistics
Downloading and uploading files using SFTP (1:40-1:50)
- The sftp and scp commands DONE
- DEMO: Using CyberDuck on the desktop
