Merge branch 'main' into patch-1

.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

episodes/05-writing-scripts.md

@@ -330,16 +330,12 @@ using a transfer program, it needs to be installed on your local machine, not yo
 
 ## Transferring Data Between your Local Machine and the Cloud
 
-If you're using Windows with PuTTY instead of Git Bash, please select the alternative option here:
-<select id="id_platform" name="platformlist" onchange="change_content_by_platform('id_platform');return false;">
+If you're using Linux, Mac OS, or Windows with Git Bash on your local machine, you can use
+`scp` to upload data to your virtual machine.
 
-<option value="unix" id="id_unix" selected> Linux, Mac OS, Git Bash </option>
-<option value="win" id="id_win"> PuTTY </option>
-</select>
+::::::::::::::: spoiler
 
-<div id="div_unix" style="display:block" markdown="1">
-
-### Uploading Data to your Virtual Machine with scp
+### SCP
 
 `scp` stands for 'secure copy protocol', and is a widely used UNIX tool for moving files
 between computers. The simplest way to use `scp` is to run it in your local terminal,
@@ -388,16 +384,19 @@ $ scp [email protected]:/home/dcuser/shell_data/untrimmed_fastq/scripted_bad_rea
 
 Remember that in both instances, the command is run from your local machine, we've just flipped the order of the to and from parts of the command.
 
-</div>
+:::::::::::::::::::::::
+
+If you are using Windows without Git Bash on your local machine, you can use `pscp.exe`
+to upload data to your virtual machine.
 
-<div id="div_win" style="display:block" markdown="1">
+::::::::::::::: spoiler
 
-### Uploading Data to your Virtual Machine with PSCP
+### PCSP
 
 If you're using a Windows PC without Git Bash, we recommend you use the *PSCP* program.
 This program is from the same suite of tools as the PuTTY program we have been using to connect.
 
-1. If you haven't done so, download pscp from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)
+1. If you haven't done so, download *PSCP* from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)
 2. Make sure the *PSCP* program is somewhere you know on your computer. In this case,
   your Downloads folder is appropriate.
 3. Open the windows [PowerShell](https://en.wikipedia.org/wiki/Windows_PowerShell);
@@ -426,13 +425,11 @@ C:\User\your-pc-username\Downloads> pscp.exe [email protected]
 C:\User\your-pc-username\Downloads
 ```
 
-</div>
+:::::::::::::::::::::::
 
 :::::::::::::::::::::::::::::::::::::::: keypoints
 
 - Scripts are a collection of commands executed together.
 - Transferring information to and from virtual and local computers.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
-
-

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 +1,84 @@
+---
+title: Etherpad template
+subtitle: Template text to paste into a collaborative document, such as Etherpad.
+
+---
+
+# Welcome to The Carpentries Etherpad!
+
+This pad is synchronized as you type, so that everyone viewing this page sees the same text. This allows you to collaborate seamlessly on documents.
+
+Use of this service is restricted to members of The Carpentries community; this is not for general purpose use (for that, try https://etherpad.wikimedia.org).
+
+Users are expected to follow our code of conduct: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+
+All content is publicly available under the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/
+
+- - - - - 
+
+# Timings
+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)
+
+## Short 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)
+
+## Long 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 and email below to confirm your attendance and mention one thing you hope to learn from this workshop.
+
+-
+-
+-
+-
+
+## 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.
+
+ [Episode 1: Introducing the Shell](https://datacarpentry.org/shell-genomics/01-introduction.html)
+
+ [Episode 2: Navigating Files and Directories](https://datacarpentry.org/shell-genomics/02-the-filesystem.html)
+
+[Episode 3: Working with Files and Directories](https://datacarpentry.org/shell-genomics/03-working-with-files.html)
+
+[Episode 4: Redirection](https://datacarpentry.org/shell-genomics/04-redirection.html)
+
+[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)
+
+## Feedback
+Link to feedback form if needed.
+
+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
+
+- - - - - 
+
+#### Please list another thing you found less useful, or that could be improved
+
+- - - - - 

instructors/instructor-notes.md

@@ -21,6 +21,12 @@ This lesson uses data hosted on an Amazon Machine Instance (AMI). Instructors wi
 
 ## Technical tips and tricks
 
+### Etherpad template
+
+There is a [template Etherpad](https://datacarpentry.org/shell-genomics/instructor/etherpad_template.html) to
+paste into a collaborative document, such as the [Carpentries Etherpad](https://pad.carpentries.org/). Etherpad
+supports synchronous document editing and is useful for collaborative work when teaching lessons.
+
 #### Command Prompt Editing
 
 Instructors might find it helpful to shorten their command prompt to allow better visibility of the commands they are typing, particularly if using the AMI.  This is because the prompt will contain additional information including the username and login for the instance, as well as filesystem location. This is especially useful when teaching the material online, as many learners may be splitting their screens and text wrapping may make the commands more difficult to identify if the prompt takes up a lot of space.