Initial commit

.github/workflows/render_page.yml

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+name: render page
+on:
+  push:
+    branches:
+      - master 
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material 
+      - run: mkdocs gh-deploy --force

.gitignore

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+.DS_Store
+site
+env/

README.md

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+# Course website template
+
+**Find instructions at [sib-swiss.github.io/gh-pages-training/](https://sib-swiss.github.io/gh-pages-training/).**
+
+This website is generated with [MkDocs](https://www.mkdocs.org/), with the theme [Material](https://squidfunk.github.io/mkdocs-material/).
+
+To host it locally, install MkDocs:
+```bash
+pip install mkdocs
+```
+
+and Material:
+```bash
+pip install mkdocs-material
+```
+
+Fork this repository and clone it to your local computer. Then, make the repository your current directory and type:
+
+```bash
+mkdocs serve
+```
+
+To host it locally.
+
+Check it out with your browser at [http://localhost:8000/](http://localhost:8000/).
+
+For an automatically generated github page, you can run:
+
+```sh
+mkdocs gh-deploy
+```
+
+This will generate a webpage at:
+
+https://yourname.github.io/reponame

docs/course_schedule.md

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+
+| start 	| end   	| topic   	|
+|-------	|-------	|---------	|
+| 10:00 	| 10:30 	| coffee! 	|
+| 12:00 	| 13:00 	| lunch!  	|
+
+Generate markdown tables at [tablesgenerator.com](https://www.tablesgenerator.com/markdown_tables)

docs/index.md

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+# Course website
+
+## Material
+
+* This website
+* Zoom meeting (through mail)
+* Google doc (through mail)
+* [Slack channel](https://slack.com)
+
+## Learning outcomes
+
+### General learning outcomes
+
+After this course, you will be able to:
+
+### Learning outcomes explained
+
+To reach the general learning outcomes above, we have set a number of smaller learning outcomes. Each chapter starts with these smaller learning outcomes. Use these at the start of a chapter to get an idea what you will learn. Use them also at the end of a chapter to evaluate whether you have learned what you were expected to learn.
+
+## Learning experiences
+
+To reach the learning outcomes we will use lectures, exercises, polls and group work. During exercises, you are free to discuss with other participants. During lectures, focus on the lecture only.
+
+### Exercises
+
+Each block has practical work involved. Some more than others. The practicals are subdivided into chapters, and we'll have a (short) discussion after each chapter. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.
+
+### Asking questions
+During lectures, you are encouraged to raise your hand if you have questions (if in-person), or use the Zoom functionality (if online). Find the buttons in the participants list ('Participants' button):
+
+<figure>
+  <img src="assets/images/zoom_icons.png" width="300"/>
+</figure>
+
+Alternatively, (depending on your zoom version or OS) use the 'Reactions' button:
+
+<figure>
+  <img src="assets/images/reactions_zoom.png" width="200"/>
+</figure>
+
+A main source of communication will be our [slack channel](https://www.slack.com). Ask background questions that interest you personally at **#background**. During the exercises, e.g. if you are stuck or don't understand what is going on, use the slack channel **#q-and-a**.  This channel is not only meant for asking questions but also for answering questions of other participants. If you are replying to a question, use the "reply in thread" option:
+
+<figure>
+  <img src="assets/images/reply_in_thread.png" width="350"/>
+</figure>
+
+The teacher will review the answers, and add/modify if necessary. If you're really stuck and need specific tutor support, write the teachers or helpers personally.
+
+**To summarise:**
+
+* During lectures: raise hand/zoom functionality
+* Personal interest questions: **#background**
+* During exercises: **\#q-and-a** on slack

docs/precourse.md

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+
+## UNIX
+
+As is stated in the course prerequisites at the [announcement web page](https://www.sib.swiss/training/), we expect participants to have a basic understanding of working with the command line on UNIX-based systems. You can test your UNIX skills with a quiz [here](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_link). If you don't have experience with UNIX command line, or if you're unsure whether you meet the prerequisites, follow our [online UNIX tutorial](https://edu.sib.swiss/pluginfile.php/2878/mod_resource/content/4/couselab-html/content.html).
+
+## Software
+
+We will be mainly working on an Amazon Web Services ([AWS](https://aws.amazon.com/))  Elastic Cloud (EC2) server. Our Ubuntu server behaves like a 'normal' remote server, and can be approached through `ssh` with a username, key and IP address. All participants will be granted access to a personal home directory.
+
+Before the course, make sure you can comfortably work on a remote server. This means that you can approach it through the shell, modify scripts and transfer files. We can recommend `atom` for Linux and Mac, and `Notepad ++` in combination with MobaXterm for Windows. We will be visualising our results with IGV. Therefore, install in your computer:
+
+=== "mac OS/Linux"
+    * SSH and scripting: [Atom](https://atom.io/) with packages like: [`terminus`](https://atom.io/packages/terminus) and [`ftp-remote-edit`](https://atom.io/packages/ftp-remote-edit)
+    * Transferring files: [FileZilla](https://filezilla-project.org/)
+    * [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/)
+
+=== "Windows"
+    * SSH and scripting: [MobaXterm](https://mobaxterm.mobatek.net/ "get MobaXterm") and/or [Notepad++](https://notepad-plus-plus.org/downloads/) with the plugin `NppFTP`
+    * Transferring files: [FileZilla](https://filezilla-project.org/)
+    * [Integrative Genomics Viewer (IGV)](http://software.broadinstitute.org/software/igv/)

docs/stylesheets/extra.css

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+:root {
+  --md-primary-fg-color:        #D40000;
+  --md-accent-fg-color:         #999999;
+}

mkdocs.yml

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+site_name: My site
+nav:
+    - Home: index.md
+    - Precourse preparations: precourse.md
+    - Course schedule: course_schedule.md
+    - Exercises: exercises.md
+
+theme:
+  name: material
+  logo: assets/images/SIB_logo.svg
+  favicon: assets/images/SIB_logo.svg
+
+# Repository
+repo_name: sib-swiss/course_website_template
+repo_url: https://github.com/sib-swiss/course_website_template
+
+markdown_extensions:
+  - abbr
+  - def_list
+  - footnotes
+  - tables
+  - admonition
+  - codehilite:
+      guess_lang: false
+  - sane_lists
+  - smarty
+  - toc
+  - pymdownx.superfences
+  - attr_list
+  - pymdownx.tabbed
+  - pymdownx.details
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+
+extra_css:
+  - stylesheets/extra.css