Make the etherpad template more generic (#353)

* Make the etherpad template more generic

* clarify purpose of etherpad template

Author: p-j-smith

instructors/etherpad_template.md

@@ -1,217 +1,67 @@
 ---
 title: Etherpad template
-subtitle: Template text to paste in to collaborative document
----
-
-# Introduction to the Command Line for Genomic
-
-**Date**
-
-**Instructor**
-
-**Helper**
-
-**Website**
-[https://datacarpentry.org/shell-genomics](https://datacarpentry.org/shell-genomics)
-
-## Timings - EDIT FOR YOUR WORKSHOP
-
-Here's a tentative schedule for the workshop
-
-- Introducing the Shell 09:30-10:00 (30 mins)
-- Navigating Files and Directories 10:00-10:50 (50 mins)
-- Break 10:50-11:05 (15 mins)
-- Working with Files and Directories 11:05-11:50 (45 mins)
-- Redirection 11:50-12:35 (45 mins)
-- Break 12:35-13:30 (55 mins)
-- Writing Scripts and Working with Data 13:30-14:10 (40 mins)
-- Project Organization 14:10-14:40 (30 mins)
-- Wrap up and feedback 14:40-14:55 (15 mins)
-
-## Attendees
-
-Please write your name below to confirm your attendance and mention one thing you hope to learn from this workshop.
-
-1.
-2.
-3.
-4. 
- 
-## Feedback
-
-Link to feedback form if needed
-
-## [Introducing the Shell](https://datacarpentry.org/shell-genomics/01-introduction.html)
-
-### Exercise:
-
-Use the `-l` option for the `ls` command to display more information for each item in the directory. 
-
-What is one piece of additional information this long format gives you that you don’t see with the bare `ls` command?
-- - -
-
-## [Navigating Files and Directories](https://datacarpentry.org/shell-genomics/02-the-filesystem.html)
-
-### Exercise: FINDING HIDDEN DIRECTORIES
-
-First navigate to the `shell_data` directory. 
-There is a hidden directory within this directory. Explore the options for `ls` to find out how to see hidden directories. 
-List the contents of the directory and identify the name of the text file in that directory.
-
-**Hint:** hidden files and folders in Unix start with ., for example .my_hidden_directory
-
-
-### Exercise: NAVIGATING PRACTICE
-
-Navigate to your home directory. From there, list the contents of the `untrimmed_fastq` directory.
-
-### Exercise: RELATIVE PATH RESOLUTION
-
-Using the filesystem diagram on the lesson page [below](https://datacarpentry.org/shell-genomics/02-the-filesystem.html), if pwd `displays` `/Users/thing`, what will ls .`./backup display`?
-
-Put a `+` next to the answer you think is correct.
-
-1. ../backup: No such file or directory
-2. 2012-12-01 2013-01-08 2013-01-27
-3. 2012-12-01/ 2013-01-08/ 2013-01-27/
-4. original pnas_final pnas_sub
-
-
-## [Working with Files and Directories](https://datacarpentry.org/shell-genomics/03-working-with-files.html)
-
-### Exercise: 
-
-Do each of the following tasks from your current directory using a single `ls` command for each:
+subtitle: Template text to paste into a collaborative document, such as Etherpad.
 
-1.  List all of the files in `/usr/bin` that start with the letter ‘c’.
-2.  List all of the files in `/usr/bin` that contain the letter ‘a’.
-3.  List all of the files in `/usr/bin` that end with the letter ‘o’.
-
-Bonus: List all of the files in `/usr/bin` that contain the letter ‘a’ or the letter ‘c’.
-
-**Hint:** The bonus question requires a Unix wildcard that we haven’t talked about yet. Try searching the internet for information about Unix wildcards to find what you need to solve the bonus problem.
-- - -
-### Exercise: echo and wildcards
-
-`echo` is a built-in shell command that writes its arguments, like a line of text to standard output. 
-The `echo` command can also be used with pattern matching characters, such as wildcard characters. 
-Here we will use the `echo` command to see how the wildcard character is interpreted by the shell.
-
-```bash
-$ echo *.fastq
-```
-What would the output look like if the wildcard could not be matched?
-
-Compare the outputs of 
-
-1. `echo *.missing` 
-2. `ls *.missing`
-- - -
-### Exercise: command history
-
-Find the line number in your `history` for the command that listed all the `.sh` files in `/usr/bin`. 
-Rerun that command.
-
-- - -
-
-### Exercise: Examining Files
-
-1. Print out the contents of the `~/shell_data/untrimmed_fastq/SRR097977.fastq` file. What is the last line of the file?
-
-2. From your home directory, and without changing directories, use one short command to print the contents of all of the files in the
-`~/shell_data/untrimmed_fastq` directory.
-
-- - -
-
-### Exercise: Examining Files
-
-Use `less` on the file SRR097977.fastq and find the next three nucleotides (characters) after the first instance of the sequence `TTTTT`?
-
-- - -
-
-### Exercise: 
-
-Starting in the `shell_data/untrimmed_fastq/` directory, do the following:
-
-1. Make sure that you have deleted your backup directory and all files it contains.
-2. Create a backup of each of your FASTQ files using cp. (Note: You’ll need to do this individually for each of the two FASTQ files. We haven’t learned yet how to do this with a wildcard.)
-3. Use a wildcard to move all of your backup files to a new backup directory.
-4. Change the permissions on all of your backup files to be write-protected.
-
-- - -
-
-## [Redirection](https://datacarpentry.org/shell-genomics/04-redirection.html)
-
-### EXERCISE:
-
-1. Search for the sequence `GNATNACCACTTCC in the `SRR098026.fastq` file. Have your search return all matching lines and the name (or identifier) for each sequence that contains a match.
-
-2. Search for the sequence `AAGTT` in both FASTQ files. Have your search return all matching lines and the name (or identifier) for each sequence that contains a match.
-- - -
-
-### EXERCISE
-
-How many sequences are there in `SRR098026.fastq`? Remember that every sequence is formed by four lines.
-
-- - -
-
-### EXERCISE
-
-How many sequences in `SRR098026.fastq` contain at least 3 consecutive Ns?
-
-- - -
-
-### EXERCISE
+---
 
-Print the file prefix of all of the `.txt` files in our current directory.
+# Timings
+Here's a tentative schedule for the workshop.
 
-- - -
+## Introducing the shell
+09:30-10:00 (30 mins)
 
-### EXERCISE
+## Navigating files and directories
+10:00-10:50 (50 mins)
 
-Remove `_2019` from all of the `.txt` files.
+## Short break
+10:50-11:05 (15 mins)
 
-- - - 
+## Working with files and directories
+11:05-11:50 (45 mins)
 
-## [Writing Scripts and Working with Data](https://datacarpentry.org/shell-genomics/05-writing-scripts.html)
+## Redirection 
+11:50-12:35 (45 mins)
 
-### EXERCISE
+## Long break
+12:35-13:30 (55 mins)
 
-Open README.txt, add the date to the top of the file, and then save it.
+## Writing scripts and working with data
+13:30-14:10 (40 mins)
 
-- - -
+## Project organization
+14:10-14:40 (30 mins)
 
-### EXERCISE
+## Wrap up and feedback 
+14:40-14:55 (15 mins)
 
-We want the script to tell us when it’s done.
+## Attendees
+Please write your name and email below to confirm your attendance and mention one thing you hope to learn from this workshop.
 
-Open `bad-reads-script.sh` and add the line echo `"Script finished!"` after the grep command and save the file.
-Run the updated script.
+-
+-
+-
+-
 
-- - -
+## Notes
+Ask your students to keep notes as you go through the lesson's content and exercises.
+Links to the episodes are provided below for quick and easy access.
 
-## [Project Organization](https://datacarpentry.org/shell-genomics/06-organization.html)
+ [Episode 1: Introducing the Shell](https://datacarpentry.org/shell-genomics/01-introduction.html)
 
-### EXERCISE
-Use the `mkdir` command to make the following directories:
+ [Episode 2: Navigating Files and Directories](https://datacarpentry.org/shell-genomics/02-the-filesystem.html)
 
-```
-dc_workshop
-dc_workshop/docs
-dc_workshop/data
-dc_workshop/results
-```
-- - -
+[Episode 3: Working with Files and Directories](https://datacarpentry.org/shell-genomics/03-working-with-files.html)
 
-### EXERCISE
+[Episode 4: Redirection](https://datacarpentry.org/shell-genomics/04-redirection.html)
 
-Using your knowledge of the shell, use the append redirect >> to create a file called `dc_workshop_log_XXXX_XX_XX.sh` (Use the four-digit year, two-digit month, and two digit day, e.g. `dc_workshop_log_2017_10_27.sh`)
+[Episode 5: Writing Scripts and Working with Data](https://datacarpentry.org/shell-genomics/05-writing-scripts.html)
 
-- - -
+[Episode 6: Project Organization](https://datacarpentry.org/shell-genomics/06-organization.html)
 
-## Evaluation and Feedback
+## Feedback
+Link to feedback form if needed.
 
-Your feedback is valuable as it helps instructors and lesson maintainers enhance the content.
+Remind students that their feedback is valuable as it helps instructors and lesson maintainers enhance the content.
 
 #### Please list one thing you liked or found particularly useful