[custom] fix lesson contents

CODE_OF_CONDUCT.md

@@ -8,6 +8,8 @@ we pledge to follow the [The Carpentries Code of Conduct][coc].
 Instances of abusive, harassing, or otherwise unacceptable behavior
 may be reported by following our [reporting guidelines][coc-reporting].
 
-
-[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
 [coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+
+
+

CONTRIBUTING.md

@@ -21,18 +21,18 @@ mistake, some awkward wording, or a factual error. This is a good way to
 introduce yourself and to meet some of our community members.
 
 1. If you do not have a [GitHub][github] account, you can [send us comments by
-   email][contact]. However, we will be able to respond more quickly if you use
-   one of the other methods described below.
+  email][contact]. However, we will be able to respond more quickly if you use
+  one of the other methods described below.
 
 2. If you have a [GitHub][github] account, or are willing to [create
-   one][github-join], but do not know how to use Git, you can report problems
-   or suggest improvements by [creating an issue][repo-issues]. This allows us
-   to assign the item to someone and to respond to it in a threaded discussion.
+  one][github-join], but do not know how to use Git, you can report problems
+  or suggest improvements by [creating an issue][repo-issues]. This allows us
+  to assign the item to someone and to respond to it in a threaded discussion.
 
 3. If you are comfortable with Git, and would like to add or change material,
-   you can submit a pull request (PR). Instructions for doing this are
-   [included below](#using-github). For inspiration about changes that need to
-   be made, check out the [list of open issues][issues] across the Carpentries.
+  you can submit a pull request (PR). Instructions for doing this are
+  [included below](#using-github). For inspiration about changes that need to
+  be made, check out the [list of open issues][issues] across the Carpentries.
 
 Note: if you want to build the website locally, please refer to [The Workbench
 documentation][template-doc].
@@ -41,8 +41,7 @@ documentation][template-doc].
 
 1. If you wish to change this lesson, add issues and pull requests here.
 2. If you wish to change the template used for workshop websites, please refer
-   to [The Workbench documentation][template-doc].
-
+  to [The Workbench documentation][template-doc].
 
 ### What to Contribute
 
@@ -80,12 +79,12 @@ Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we
 use [GitHub flow][github-flow] to manage changes:
 
 1. Create a new branch in your desktop copy of this repository for each
-   significant change.
+  significant change.
 2. Commit the change in that branch.
 3. Push that branch to your fork of this repository on GitHub.
 4. Submit a pull request from that branch to the [upstream repository][repo].
 5. If you receive feedback, make changes on your desktop and push to your
-   branch on GitHub: the pull request will update automatically.
+  branch on GitHub: the pull request will update automatically.
 
 NB: The published copy of the lesson is usually in the `main` branch.
 
@@ -98,26 +97,26 @@ final say over what gets merged into the lesson.
 The Carpentries is a global organisation with volunteers and learners all over
 the world. We share values of inclusivity and a passion for sharing knowledge,
 teaching and learning. There are several ways to connect with The Carpentries
-community listed at <https://carpentries.org/connect/> including via social
+community listed at [https://carpentries.org/connect/](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-issues]: https://example.com/FIXME/issues
-[contact]: mailto:[email protected]
 [cp-site]: https://carpentries.org/
-[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
-[dc-lessons]: https://datacarpentry.org/lessons/
+[swc-site]: https://software-carpentry.org/
 [dc-site]: https://datacarpentry.org/
-[discuss-list]: https://carpentries.topicbox.com/groups/discuss
+[lc-site]: https://librarycarpentry.org/
 [github]: https://github.com
-[github-flow]: https://guides.github.com/introduction/flow/
+[contact]: mailto:[email protected]
 [github-join]: https://github.com/join
-[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[repo-issues]: https://github.com/datacarpentry/genomics-workshop/issues
 [issues]: https://carpentries.org/help-wanted-issues/
+[template-doc]: https://carpentries.github.io/workbench/
+[dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [lc-issues]: https://github.com/issues?q=user%3ALibraryCarpentry
 [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry
-[swc-lessons]: https://software-carpentry.org/lessons/
-[swc-site]: https://software-carpentry.org/
-[lc-site]: https://librarycarpentry.org/
-[template-doc]: https://carpentries.github.io/workbench/
+[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[github-flow]: https://guides.github.com/introduction/flow/
+[repo]: https://github.com/datacarpentry/genomics-workshop
+
+
+

LICENSE.md

@@ -12,8 +12,8 @@ license][cc-by-legal].
 
 You are free:
 
-- to **Share**---copy and redistribute the material in any medium or format
-- to **Adapt**---remix, transform, and build upon the material
+- to **Share**\---copy and redistribute the material in any medium or format
+- to **Adapt**\---remix, transform, and build upon the material
 
 for any purpose, even commercially.
 
@@ -22,30 +22,30 @@ terms.
 
 Under the following terms:
 
-- **Attribution**---You must give appropriate credit (mentioning that your work
+- **Attribution**\---You must give appropriate credit (mentioning that your work
   is derived from work that is Copyright (c) The Carpentries and, where
-  practical, linking to <https://carpentries.org/>), provide a [link to the
+  practical, linking to [https://carpentries.org/](https://carpentries.org/)), provide a [link to the
   license][cc-by-human], and indicate if changes were made. You may do so in
   any reasonable manner, but not in any way that suggests the licensor endorses
   you or your use.
 
-- **No additional restrictions**---You may not apply legal terms or
+- **No additional restrictions**\---You may not apply legal terms or
   technological measures that legally restrict others from doing anything the
   license permits.  With the understanding that:
 
 Notices:
 
-* You do not have to comply with the license for elements of the material in
+- You do not have to comply with the license for elements of the material in
   the public domain or where your use is permitted by an applicable exception
   or limitation.
-* No warranties are given. The license may not give you all of the permissions
+- No warranties are given. The license may not give you all of the permissions
   necessary for your intended use. For example, other rights such as publicity,
   privacy, or moral rights may limit how you use the material.
 
 ## Software
 
 Except where otherwise noted, the example programs and other software provided
-by The Carpentries are made available under the [OSI][osi]-approved [MIT
+by The Carpentries are made available under the [OSI][osi]\-approved [MIT
 license][mit-license].
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
@@ -74,6 +74,9 @@ Initiatives][ci].
 
 [cc-by-human]: https://creativecommons.org/licenses/by/4.0/
 [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[osi]: https://opensource.org
 [mit-license]: https://opensource.org/licenses/mit-license.html
 [ci]: https://communityin.org/
-[osi]: https://opensource.org
+
+
+

config.yaml

@@ -14,7 +14,7 @@ carpentry: 'dc'
 title: 'Genomics Workshop Overview'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: ~ # FIXME
+created: '2015-06-03'
 
 # Comma-separated list of keywords for the lesson
 keywords: 'software, data, lesson, The Carpentries' # FIXME

index.md

@@ -20,7 +20,6 @@ Interested in teaching these materials? We have an [onboarding video](https://ww
 
 Read our [FAQ](/genomics-workshop/faq) to learn more about Data Carpentry's Genomics workshop, as an Instructor or a workshop host.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::::::::  prereq
@@ -46,13 +45,12 @@ This workshop uses data from a long term evolution experiment published in 2016:
 All of the data used in this workshop can be [downloaded from Figshare](https://figshare.com/articles/Data_Carpentry_Genomics_beta_2_0/7726454).
 More information about this data is available on the [Data page](https://datacarpentry.org/organization-genomics/data/).
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 # Workshop Overview
 
 | Lesson | Overview                                                                                                                                                                      | 
-| ------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ----------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------ |
 | [Project organization and management](https://datacarpentry.github.io/organization-genomics/)       | Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. | 
 | [Introduction to the command line](https://datacarpentry.github.io/shell-genomics/)       | Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.                          | 
 | [Data wrangling and processing](https://datacarpentry.github.io/wrangling-genomics/)       | Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation.                                    | 
@@ -61,7 +59,7 @@ More information about this data is available on the [Data page](https://datacar
 # Optional Additional Lessons
 
 | Lesson | Overview                                                                                                                                                                      | 
-| ------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ----------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------ |
 | [Intro to R and RStudio for Genomics](https://datacarpentry.org/genomics-r-intro/)       | Use R to analyze and visualize between-sample variation.                                                                                                                      | 
 
 # Teaching Platform

instructors/AMI-setup.md

@@ -27,7 +27,6 @@ you will need to create your own AMI instances using the instructions below. The
 t2.medium instance type is about USD $1.20 per day. Data Carpentry has no control over AWS pricing structure and provides
 this cost estimate with no guarantees. Please see the [EC2 pricing page](https://aws.amazon.com/ec2/pricing/on-demand) for up-to-date information.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ### Launching an instance on Amazon Web Services
@@ -38,8 +37,7 @@ this cost estimate with no guarantees. Please see the [EC2 pricing page](https:/
 
 - Form of payment (credit card)
 - Understanding of Amazon's billing and payment (See: [Getting started with AWS Billing and Cost Management](https://docs.aws.amazon.com/awsaccountbilling/latest/aboutv2/billing-getting-started.html))
-- You can use some of Amazon Web Services for free, or see if you qualify for an AWS Grant (See: [https://aws.amazon.com/grants/](https://aws.amazon.com/grants/) ) if you are using AWS for education. The free level of service *will not* be sufficient for working with the amount of data we are using for our lessons.  
-
+- You can use some of Amazon Web Services for free, or see if you qualify for an AWS Grant (See: [https://aws.amazon.com/grants/](https://aws.amazon.com/grants/) ) if you are using AWS for education. The free level of service *will not* be sufficient for working with the amount of data we are using for our lessons.
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
@@ -57,7 +55,7 @@ this cost estimate with no guarantees. Please see the [EC2 pricing page](https:/
 
 <img src="fig/logging-onto-cloud_1.png" width="500" alt="Screenshot of AWS EC2 dashboard showing location of launch instance button.">
 
-3\. Under 'Application and OS Images (Amazon Machine Image)' search for the AMI listed on this curriculum's [Setup page](https://datacarpentry.org/genomics-workshop/setup.html)
+3\. Under 'Application and OS Images (Amazon Machine Image)' search for the AMI listed on this curriculum's [Setup page](https://datacarpentry.org/genomics-workshop/index.html#setup)
 
 <img src="fig/logging-onto-cloud_1b.png" width="500" alt="Screenshot of AMI launch wizard showing search function.">
 
@@ -104,7 +102,7 @@ Your security group should now look like this:
 You instance will now be launched. You should follow the links to 'Create billing alerts' and then the instructions below
 for connecting to and terminating your Amazon Instance.
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Connect to your Amazon Instance (MacOS/Linux)
 
@@ -149,7 +147,7 @@ $ pwd
 
 :::::::::::::::::::::::::
 
-:::::::::::::::  solution
+:::::::::::::::: spoiler
 
 ## Connect to your Amazon instance (Windows)
 
@@ -195,7 +193,6 @@ charge from your AWS EC2 dashboard by clicking your name (Account
 name) on the upper right of the dashboard and selecting 'Billing
 \& Cost Management'. **DO NOT FORGET TO TERMINATE YOUR INSTANCE WHEN YOU ARE DONE**
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 When you are finished with your instance, you must terminate it to avoid unwanted charges. Follow the following steps.
@@ -212,7 +209,6 @@ When you are finished with your instance, you must terminate it to avoid unwante
 
 Terminating an instance will delete any data on this instance, so you must move any data you wish to save off the instance.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 5. Select 'Terminate' to terminate the instance.

instructors/instructor-notes.md

@@ -19,7 +19,7 @@ centrally-organized Carpentries workshops.
 #### Installation
 
 This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. See the
-[Setup page](https://datacarpentry.org/genomics-workshop/setup.html) for complete setup instructions. If you are
+[Setup page](https://datacarpentry.org/genomics-workshop/index.html#setup) for complete setup instructions. If you are
 teaching these lessons, and would like an AWS instance to practice on, please contact [[[email protected]](mailto:[email protected])](mailto: [[email protected]](mailto:[email protected])).
 
 ## Common problems