Scripting

[sr320]

Create either a script, jupyter notebook, or R markdown file that performs a relevant operation(s) on a number of files (>4) "automatically".

This should be in your class repo and should be written in a manner that when I clone the repo I can generate the output.

For instance the files will need to be in the repo or the script will need to be able to pull them from a public url. Note absolute paths will not work.

please place the url to the script, jupyter notebook, or R markdown file below.

[kcribari]

Jupyter Notebook

[hgloiselle]

Jupyter notebook to run bowtie2

[yaaminiv]

R Markdown file for running methylKit

[Jeremyfishb]

Week 6 quiz script

[calderatta]

week 6 quiz repo

[wsano16]

week 6 quiz Jupyter Notebook

[melodysyue]

week 6 quiz script

[jgardn92]

My script which downloads a zipped filed containing two metadata files and an image stack, extracts variables from one of the metadata files, and then renames all the files in the image stack and rezips it. Script is not part of my class project but is needed for separate project

[laurahspencer]

quiz script

Downloads files that match a certain pattern from Owl and creates a text file listing them - should clone the repo then execute script via: bash scripts/scripting-quiz.sh

[grace-ac]

jupyter notebook

[kimh11]

My script.

This creates a list of samtools commands to convert sam to bam files for all .sam files in the folder and writes them to another file.

The actual .sam files were too big to put on GitHub, so I created placeholder files with the same names. I will be running the scripts on Mox.