1. 1 Applied CyberInfrastructure Concepts ISTA 420/520 Fall 2015 1 Nirav Merchant (nirav@email.arizona.edu) Bio Computing & iPlant Collaborative Eric Lyons (ericlyons@email.arizona.edu) Plant Sciences & iPlant Collaborative University of Arizona http://goo.gl/p4j3mhttp://goo.gl/p4j3m or https://sites.google.com/site/appliedciconcepts/ Will Computers Crash Genomics? Science Vol 331 Feb 2011

2. Tasks for today  Get familiar with Docker command line  Have fun experimenting with options  Some guidelines for todays hands on session

3. REMEMBER  There are many many cool features in Docker, remember we are not going into “rabbit holes” today Attribution unknown, obtained from: http://www.naturopathicdiaries.com/getting-rabbit-hole/

4. Guidelines for session  If you do not have docker running in your laptop or inside virtual box ubuntu, please team up  If you are not confident that you can do this on your own, please team up  We will be doing this in 10 min time box with 5 min discussion, if you are finished with the task help someone  Feel free to explore what else you can do with the commands you have learned

5. Tasks for today  10 min tutorial and walk through (instructor guided)  Define and scope the problem space we want to focus on today (10 min)  Cheat sheet https://coderwall.com/p/2es5jwhttps://coderwall.com/p/2es5jw  http://docs.docker.com/userguide/  Getting a image (busybox and others)  Running specific commands  Managing container (connect, commit and remove)  Managing images

6. Quick overview  Take a tour of docker hub and learn how to identify images you want to use  Where do images come from ? Where is it on my computer ?  What is this container business ?  Why docker files are important

7. Use case backup  Colleague gave me script to split DNA sequence into smaller chunk https://raw.githubusercontent.com/bioperl/bio perl-live/master/scripts/seq/bp_split_seq.pl https://raw.githubusercontent.com/bioperl/bio perl-live/master/scripts/seq/bp_split_seq.pl  Need bioperl and many other things …  Here is the sequence I need to split http://greengenes.lbl.gov/Data/JD_Tutorial/Un AligSeq24606.txt http://greengenes.lbl.gov/Data/JD_Tutorial/Un AligSeq24606.txt  HELP