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Week 2: Tech Resources and Commands

Resources for working with Linux, Python, and your Raspberry Pi

CGRB Jupyter Hub: (this will disappear after camp; please be sure to download your Notebook files)

Python3 Language Documentation (and tutorials):

Raspberry Pi (main site):

Raspberry Pi Docs:

Raspbian Documentation:

Linux Commands for installing needed modules/libraries/applications: 

  • MatPlotLib (Python graphing and plotting tools): sudo pip3 install matplotlib
  • BioPython (Python bioinformatics packages): sudo pip3 install biopython
  • ClustalW (Linux genetic sequence clustering program): sudo apt-get install clustalw

Helpful Linux commands for your Pi:

  • Download & install open-source software: sudo apt-get install <package_name>
  • Download & install python modules/libraries: sudo pip3 install <module_name>
  • Launch your local Jupyter Notebook: jupyter notebook
  • Shutdown your Pi: sudo shutdown -h now (can also be done from the Raspbian GUI menu)

Crown Gall Microbiome analysis output files:

If you have any questions about Python or running your Raspberry Pi, please contact preecej[at]science[dot]oregonstate[dot]edu.