Resources for working with Linux, Python, and your Raspberry Pi
CGRB Jupyter Hub: https://web-dev.cgrb.oregonstate.edu/J-STEM/hub/login (this will disappear after camp; please be sure to download your Notebook files)
Python3 Language Documentation (and tutorials): https://docs.python.org/3.4/
Raspberry Pi (main site): https://www.raspberrypi.org
Raspberry Pi Docs: https://www.raspberrypi.org/documentation/
Raspbian Documentation: https://www.raspbian.org/
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:
http://changlab.cgrb.oregonstate.edu/sites/default/files/PCoA_plot.png
http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_class…
http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_order…
http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_famil…
http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_phylu…
http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_genus…
If you have any questions about Python or running your Raspberry Pi, please contact preecej[at]science[dot]oregonstate[dot]edu.