From 96dfd7dccec45642ef8b6f0fb3147cb5b98764d1 Mon Sep 17 00:00:00 2001 From: "Zhian N. Kamvar" Date: Tue, 19 Sep 2023 11:51:32 -0700 Subject: [PATCH] [custom] fix lesson contents --- CODE_OF_CONDUCT.md | 6 ++-- CONTRIBUTING.md | 49 ++++++++++++++++----------------- LICENSE.md | 21 ++++++++------ config.yaml | 2 +- index.md | 6 ++-- instructors/AMI-setup.md | 12 +++----- instructors/instructor-notes.md | 2 +- learners/setup.md | 38 +++++++++++-------------- 8 files changed, 64 insertions(+), 72 deletions(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f19b8049..25bd0a84 100644 --- a/CODE_OF_CONDUCT.md +++ b/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 + + + diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6c2b81c8..06cff02d 100644 --- a/CONTRIBUTING.md +++ b/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 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:team@carpentries.org [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:team@carpentries.org [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 + + + diff --git a/LICENSE.md b/LICENSE.md index 7632871f..ff328255 100644 --- a/LICENSE.md +++ b/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 ), 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 + + + diff --git a/config.yaml b/config.yaml index f9f534ee..b50cf75d 100644 --- a/config.yaml +++ b/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 diff --git a/index.md b/index.md index f2bfbab8..67bcab18 100644 --- a/index.md +++ b/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 diff --git a/instructors/AMI-setup.md b/instructors/AMI-setup.md index d2ec5350..61600214 100644 --- a/instructors/AMI-setup.md +++ b/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:/ 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) 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. diff --git a/instructors/instructor-notes.md b/instructors/instructor-notes.md index 00015705..be69210a 100644 --- a/instructors/instructor-notes.md +++ b/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 [[team@carpentries.org](mailto:team@carpentries.org)](mailto: [team@carpentries.org](mailto:team@carpentries.org)). ## Common problems diff --git a/learners/setup.md b/learners/setup.md index b646bfc5..b5b147f7 100644 --- a/learners/setup.md +++ b/learners/setup.md @@ -23,7 +23,7 @@ It's a free, open source spreadsheet program. Directions to install are included for each Windows, Mac OS X, and Linux systems below. For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu Subsystem. -::::::::::::::: solution +:::::::::::::::: spoiler ## Windows @@ -71,11 +71,10 @@ For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu - **Another alternative option** is to use the Ubuntu Subsystem for Windows. This option is only available for Windows 10 - the Microsoft documentation provides [detailed instructions for installing Windows 10](https://docs.microsoft.com/en-us/windows/wsl/install-win10). - ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## Mac OS X @@ -85,11 +84,10 @@ For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically. - Once the installer is downloaded, double click on it and LibreOffice should install. - ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## Linux @@ -99,7 +97,6 @@ For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically. - Once the installer is downloaded, double click on it and LibreOffice should install. - ::::::::::::::::::::::::: @@ -172,7 +169,7 @@ For more information on Miniconda, please refer to the Conda [documentation](htt ### Conda -::::::::::::::: solution +:::::::::::::::: spoiler ## Linux @@ -185,10 +182,9 @@ $ bash Miniconda3-latest-Linux-x86_64.sh Then, follow the instructions that you are prompted with on the screen to install Conda. - ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -201,12 +197,11 @@ $ bash Miniconda3-latest-MacOSX-x86_64.sh Then, follow the instructions that you are prompted with on the screen to install Conda. - ::::::::::::::::::::::::: ### FastQC -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -218,7 +213,7 @@ $ conda install -c bioconda fastqc=0.11.9 ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## FastQC Source Code Installation @@ -255,7 +250,7 @@ $ fastqc -h ### Trimmomatic -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -265,7 +260,7 @@ conda install -c bioconda trimmomatic=0.39 ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## Trimmomatic Source Code Installation @@ -298,7 +293,7 @@ $ ls ~/src/Trimmomatic-0.39/adapters/ $ java -jar ~/src/Trimmomatic-0.39/trimmomatic-0.39.jar ``` -::::::::::::::: solution +:::::::::::::::: spoiler ## Simplify the Invocation, or to Test your installation if you installed with miniconda3: @@ -320,7 +315,7 @@ $ trimmomatic ### BWA -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -330,7 +325,7 @@ conda install -c bioconda bwa=0.7.17=ha92aebf_3 ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## BWA Source Code Installation @@ -355,7 +350,7 @@ $ bwa ### SAMtools -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -374,10 +369,9 @@ But this means that most of the tutorials on the web indicate an older and obsol Using SAMtools version 1.9 is important to work with the commands we present in these lessons. - :::::::::::::::::::::::::::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## SAMtools Source Code Installation @@ -408,7 +402,7 @@ $ samtools ### BCFtools -::::::::::::::: solution +:::::::::::::::: spoiler ## MacOS @@ -418,7 +412,7 @@ $ conda install -c bioconda bcftools=1.9 ::::::::::::::::::::::::: -::::::::::::::: solution +:::::::::::::::: spoiler ## BCF tools Source Code Installation