Automation Workshop Welcome

Welcome to the automation workshop at the 6th Argonne Soils Meeting.

Schedule

Day	Schedule
Friday 10/03	1:30pm-5:00pm: Automating things with the shell (Will Trimble) Introducing the Shell (What is going on?) Files and Directories (cd,ls) Creating Things (mv,rm,cp) Pipes and Filters Loops (for) Shell Scripts (Doing Stuff) Finding Things (find,grep)
Saturday 10/04	9:00 Introduction (Adina Howe) 9:30 MEGAN (Daniel Huson) 11:30 MG-RAST website(Folker Meyer) 12:00 MG-RAST API(Daniel Braithwaite) install-matR.txt 12:30-1:30 Lunch 1:30 KBase – metabolic models for metagenomes (Chris Henry) 2:30-5:00pm Cloud computing to do more (Will Trimble) Notes on cloud computing Getting started with EC2: Logging into your new instance “in the cloud” Lecture notes on BLAST Similarity search: Basic EC2, command line, and BLAST (Lengthy lecture notes on short read mapping) Short read mapping: Mapping with bwa

Additional Resources

These bash lessons were adapted from Software Carpentry’s bash for beginners lessons. Software Carpentry is a nonprofit that maintains computational training materials for scientists.

The cloud computing lessons were adapted from GED’s ANGUS course which is run at MSU every summer and teaches workshops like this. Specifically, this is a one-afternoon abbreviation of the 2013 CEMI workshop at Caltech, which was a four-day course.