Merge branch 'main' into patch-2

.github/workflows/README.md

@@ -96,7 +96,7 @@ are okay.
 
 This update is run ~~weekly or~~ on demand.
 
-### 03 Maintain: Update Pacakge Cache (update-cache.yaml)
+### 03 Maintain: Update Package Cache (update-cache.yaml)
 
 For lessons that have generated content, we use {renv} to ensure that the output
 is stable. This is controlled by a single lockfile which documents the packages

.github/workflows/sandpaper-version.txt

@@ -1 +1 @@
-0.11.16
+0.13.0

CONTRIBUTING.md

@@ -101,7 +101,7 @@ community listed at <https://carpentries.org/connect/> including via social
 media, slack, newsletters, and email lists. You can also [reach us by
 email][contact].
 
-[repo]: https://example.com/FIXME
+[repo]: https://github.com/datacarpentry/shell-genomics
 [contact]: mailto:[email protected]
 [cp-site]: https://carpentries.org/
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
@@ -111,7 +111,7 @@ email][contact].
 [github]: https://github.com
 [github-flow]: https://guides.github.com/introduction/flow/
 [github-join]: https://github.com/join
-[how-contribute]: https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github
+[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
 [issues]: https://carpentries.org/help-wanted-issues/
 [lc-issues]: https://github.com/issues?q=user%3ALibraryCarpentry
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3260560.svg)](https://doi.org/10.5281/zenodo.3260560)
 
-[![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/)
-[![Slack Status](https://img.shields.io/badge/Slack_Channel-dc--genomics-E01563.svg)](https://swcarpentry.slack.com/messages/C9N1K7DCY)
+[![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://slack-invite.carpentries.org/)
+[![Slack Status](https://img.shields.io/badge/Slack_Channel-dc--genomics-E01563.svg)](https://carpentries.slack.com/messages/C9N1K7DCY)
 
 # Shell Genomics lessons
 

episodes/01-introduction.md

@@ -65,8 +65,7 @@ would take up time even more time. A 'ready-to-go' server lets us focus on learn
 
 ## How to access the remote server
 
-You can log-in to the remote server using the instructions
-[here](https://datacarpentry.org/cloud-genomics/02-logging-onto-cloud#logging-onto-a-cloud-instance).
+You can log-in to the remote server using the [instructions from the Introduction to Cloud Computing for Genomics lesson](https://datacarpentry.org/cloud-genomics/02-logging-onto-cloud#logging-onto-a-cloud-instance).
 Your instructor will supply to you the `ip_address` and password that you need to login.
 
 Each of you will have a different `ip_address`. This will

index.md

@@ -2,8 +2,6 @@
 site: sandpaper::sandpaper_site
 ---
 
-{% include gh\_variables.html %}
-
 Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer's operating system. They have different pros and cons. Most people are familiar with the GUI as it is the default interface for most software, particularly on Windows and Mac OS. When using the GUI, you see and interact with visual representations of files, folders, applications, and most other functions of your computer.
 When using the CLI, you work largely with text representations of software, files, folders, input and output.
 The *shell* is a program that allows you to control your computer by typing instructions on the CLI with a keyboard.

instructors/etherpad_template.md

@@ -0,0 +1,222 @@
+---
+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:
+
+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.
+
+- - -
+
+### EXERCISE
+
+Remove `_2019` from all of the `.txt` files.
+
+- - - 
+
+## [Writing Scripts and Working with Data](https://datacarpentry.org/shell-genomics/05-writing-scripts.html)
+
+### EXERCISE
+
+Open README.txt, add the date to the top of the file, and then save it.
+
+- - -
+
+### EXERCISE
+
+We want the script to tell us when it’s done.
+
+Open `bad-reads-script.sh` and add the line echo `"Script finished!"` after the grep command and save the file.
+Run the updated script.
+
+- - -
+
+## [Project Organization](https://datacarpentry.org/shell-genomics/06-organization.html)
+
+### EXERCISE
+Use the `mkdir` command to make the following directories:
+
+```
+dc_workshop
+dc_workshop/docs
+dc_workshop/data
+dc_workshop/results
+```
+- - -
+
+### EXERCISE
+
+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`)
+
+- - -
+
+## Evaluation and Feedback
+
+Your feedback is valuable as it helps instructors and lesson maintainers enhance the content.
+
+#### Please list one thing you liked or found particularly useful
+
+- - - - - 
+
+#### Please list another thing you found less useful, or that could be improved
+
+- - - - -