Scripting

[sr320]

For this week, write a bash script (.sh file) that does something practical to files you are working with for your project. Make sure it has

• a robust bash header
• variables to be set at the top of the file
• if statement
• comments indicating what each part of the script does (using #)

And at least one of the following

• Bash array
• unix program basename
• find
• xargs
• make

Add the script to your course repo, then create a jupyter notebook where you run the script and demonstrate the successful completion of the tasks.

Add the url to the Jupyter notebook below

[yaaminiv]

notebook

[jldimond]

https://github.com/jldimond/jldimond-fish546-2016/blob/master/notebooks/ipyrad_script.ipynb

[Ellior2]

https://github.com/Ellior2/Fish-546-Bioinformatics/blob/master/notebooks/script_quiz/001-Bash_Script.ipynb

[mfisher5]

Bash script notebook

[aspanjer]

https://github.com/aspanjer/RNAseq_Coho/blob/master/jupyter_notebooks/Bash%20Script.ipynb

[nclowell]

bash script notebook

[mmiddleton]

https://github.com/mmiddleton/mmiddleton-fish546/blob/master/quiz_exercises/Week9_bashscript/Week9_bashscript_notebook.ipynb

[MeganEDuffy]

bash script notebook

[laurahspencer]

Laura's Notebook!