Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create Intermediate_I_schedule.md #28

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 45 additions & 0 deletions Intermediate_shell/lessons/Intermediate_I_schedule.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
## Intermediate bash I

| Audience | Computational skills required | Duration |
:----------|:----------|:----------|
| Biologists | [Beginner bash](https://hbctraining.github.io/Training-modules/Intro_shell/) | 2-3 hour workshop (~2-3 hours of trainer-led time) |


### Description

This repository has teaching materials for a **3 hour**, hands-on **Intermediate bash** workshop led at a relaxed pace. Many tools for the analysis of big data require knowledge of the command line, and this workshop will build on the basic skills taught in the **Introduction to the command-line interface** workshop to allow for greater automation using scripts. **Add more here**

### Learning Objectives

* Define what a variable is and store information using variables
* Distinguish between variables and positional parameters
* Create a script to run multiple commands as a single command
* Implement loops, positional parameters and variables in a bash script
* Run existing R and python scripts via the command-line

> These materials are developed for a trainer-led workshop, but also amenable to self-guided learning.


### Contents

| Lessons | Estimated Duration |
|:------------------------|:----------|
|[Setting up](https://hbctraining.github.io/Training-modules/Intermediate_shell/lessons/setting_up.html) | 15 min |
|[Shell Scripts and `for` loops](https://hbctraining.github.io/Training-modules/Intermediate_shell/lessons/loops_and_scripts.html) | 75 min |
|[Positional Parameters](https://hbctraining.github.io/Training-modules/Intermediate_shell/lessons/positional_params.html) | 45 min |
|[Running R scripts and Python scripts undrafted]() |30 min |

### Dataset

[Introduction to Shell: Dataset](https://github.com/hbctraining/Training-modules/blob/master/Intro_shell/data/unix_lesson.zip?raw=true)

### Installation Requirements

***Mac users:***
[R](https://cran.r-project.org/)


***Windows users:***
[GitBash](https://git-scm.com/download/win)
[R](https://cran.r-project.org/)