Updates Containerization lesson for 2023

Lesson-02.qmd

@@ -2,7 +2,7 @@
 title: "Biostat 823 - Containerization"
 author: "Hilmar Lapp"
 institute: "Duke University, Department of Biostatistics & Bioinformatics"
-date: "Fall 2022"
+date: "Sep 14, 2023"
 format:
   revealjs:
     slide-number: true
@@ -200,10 +200,18 @@ Requires bind mount at container runtime (`docker run`):
 * Can be used for directories and files
 * Using `--mount` generates an error if target directory (or file) doesn't exist
 
-## Resources
+## Resources (I)
 
 * [Dockerfile reference](https://docs.docker.com/engine/reference/builder/)
 * [Docker command line reference](https://docs.docker.com/engine/reference/commandline/cli/)
 * [Singularity file reference](https://docs.sylabs.io/guides/latest/user-guide/definition_files.html)
 * [Singularity command line reference](https://docs.sylabs.io/guides/latest/user-guide/cli.html)
-* [Open Containers Initiative (OCI) standard for annotations](https://github.com/opencontainers/image-spec/blob/main/annotations.md)
+* [Open Containers Initiative (OCI) standard for annotations](https://github.com/opencontainers/image-spec/blob/main/annotations.md)
+
+## Resources (II)
+
+* [Introduction to Docker](https://carpentries-incubator.github.io/docker-introduction/) (Carpentries Incubator lesson)
+* [DCC OnDemand](https://dcc-ondemand-01.oit.duke.edu/)
+* [Jupyter Docker Stacks](https://jupyter-docker-stacks.readthedocs.io/)
+  - Customized [Biostat Jupyter Docker container](https://github.com/Duke-GCB/biostat-jupyter)
+* [Biostat-823 "everything" GPU container](https://gitlab.oit.duke.edu/owzar001/bios-823-container-gpu/-/blob/main/README.md) (Singularity)

pub/Lesson-02_files/libs/revealjs/plugin/highlight/plugin.js

@@ -106,7 +106,7 @@ const Plugin = {
 
 			var scrollState = { currentBlock: block };
 
-			// If there is at least one highlight step, generate
+			// If there is more than one highlight step, generate
 			// fragments
 			var highlightSteps = Plugin.deserializeHighlightSteps( block.getAttribute( 'data-line-numbers' ) );
 			if( highlightSteps.length > 1 ) {
@@ -142,7 +142,7 @@ const Plugin = {
 
 				} );
 
-				block.removeAttribute( 'data-fragment-index' )
+				block.removeAttribute( 'data-fragment-index' );
 				block.setAttribute( 'data-line-numbers', Plugin.serializeHighlightSteps( [ highlightSteps[0] ] ) );
 
 			}

pub/Lesson-02_files/libs/revealjs/plugin/markdown/plugin.js

@@ -4,7 +4,7 @@
  * of external markdown documents.
  */
 
-import marked from 'marked'
+import { marked } from 'marked';
 
 const DEFAULT_SLIDE_SEPARATOR = '\r?\n---\r?\n',
 	  DEFAULT_NOTES_SEPARATOR = 'notes?:',

pub/Lesson-02_files/libs/revealjs/plugin/math/mathjax3.js

@@ -56,7 +56,7 @@ export const MathJax3 = () => {
             let revealOptions = deck.getConfig().mathjax3 || {};
             let options = {...defaultOptions, ...revealOptions};
             options.tex = {...defaultOptions.tex, ...revealOptions.tex}
-            options.options = {...options.options, ...defaultOptions.options}
+            options.options = {...defaultOptions.options, ...revealOptions.options}
             options.startup = {...defaultOptions.startup, ...revealOptions.startup}
 
             let url = options.mathjax || 'https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js';