update to quarto

2025-11-30 09:45:43 -08:00 · 2025-09-26 20:12:30 -07:00 · 2025-09-26 20:12:30 -07:00 · 275b121c78
commit 275b121c78
parent 45cb69a732
165 changed files with 13677 additions and 4580 deletions
--- a/working-on-wynton-hpc/.Rprofile
+++ b/working-on-wynton-hpc/.Rprofile
@ -1 +0,0 @@
-source("renv/activate.R")
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_1.qmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_1.qmd
@ -1,33 +1,29 @@
 ---
 title: "Working on Wynton"
 subtitle: "Part 1"
-author: "Natalie Elphick"
-date: "March 24th, 2025"
-knit: (function(input, ...) {
-    rmarkdown::render(
-      input,
-      output_dir = "../docs"
-    )
-  })
-output:
-  revealjs::revealjs_presentation:
-    theme: simple
+author: "Natalie Gill"
+institute: "Gladstone Bioinformatics Core"
+date: "October 2, 2025"
+date-format: MMMM DD, YYYY
+format:
+  revealjs:
+    theme: wynton-theme.scss
    highlight: default
-    css: style.css
+    template-partials:
+      - title-slide.html
 ---
-
 ```{r, setup, include=FALSE}
 knitr::opts_chunk$set(comment = "")
 ```

-## 
+##

 <center>*Press the ? key for tips on navigating these slides*</center>

 ## Introductions
-Instructor:

-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**Natalie Elphick**   
+
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**Natalie Gill**   
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*Bioinformatician II*


@ -46,16 +42,16 @@ Instructor:

 # What is Wynton HPC?

-## High-performance Computing Cluster {.smaller-picture}
+## High-performance Computing Cluster

 -   A collection of specialized computers (nodes) connected together on a fast local network

-![HPC Diagram](slide_materials/HPC_diagram.png)
+![](slide_materials/HPC_diagram.png){fig-alt="HPC Diagram showing nodes connected together" .nostretch fig-align="center" width=55%}


-## HPC File System {.smaller-picture}
+## HPC File System

-![HPC File System](slide_materials/file_system_node_relationship.png)
+![](slide_materials/file_system_node_relationship.png){fig-alt="HPC File System diagram showing relationship between nodes and storage" .nostretch fig-align="center" width=60%}



@ -94,8 +90,8 @@ log1, log2 and plog1 (for PHI users)

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo "{local}$ ssh alice@log1.wynton.ucsf.edu
-alice@log1.wynton.ucsf.edu's password: 
-[alice@log1 ~]$" 
+alice@log1.wynton.ucsf.edu's password:
+[alice@log1 ~]$"
 ```

 -   There will not be any visual feedback when typing your password
@ -109,7 +105,7 @@ alice@log1.wynton.ucsf.edu's password:
 -   Cannot SSH in to directly, only from a login node

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
-echo "ssh dev1" 
+echo "ssh dev1"
 ```

 <u>Names</u>:
@ -126,7 +122,7 @@ dev[1-3], gpudev1, pdev1 (PHI) and pgpudev1 (PHI)
 <u>Example</u>:

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
-echo "{local}$ scp local_file.tsv alice@dt1.wynton.ucsf.edu:~/" 
+echo "{local}$ scp local_file.tsv alice@dt1.wynton.ucsf.edu:~/"
 ```

 <u>Names</u>:
@ -140,7 +136,7 @@ dt1 and dt2
 -   Used to run non-interactive compute job scripts
 -   The software to run the job script is provided using a container

-![Compute Jobs](slide_materials/compute_job_workflow.png)
+![](slide_materials/compute_job_workflow.png){fig-alt="Compute Jobs workflow diagram" .nostretch fig-align="center" width=65%}

 # Storage

@ -188,10 +184,10 @@ echo 'beegfs-ctl --getquota --storagepoolid=12 --gid "$(id --group)"'
 ## Storage Advice {.small-bullets}

 -   Always back up anything you store under **/wynton**
-   If you have access to it keep all of your data on **/gladstone** 
+-   If you have access to it keep all of your data on **/gladstone**
    -   A large number of jobs reading and writing to these directories may be slower since it is NFS mounted not BeeGFS
 -   Use the scratch directories to store temporary files
-    -   e.g. A large amount of .fastq that you do not need after the alignment step 
+    -   e.g. A large amount of .fastq that you do not need after the alignment step

 # Data Transfer

@ -223,7 +219,6 @@ echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destinatio



-
 ## GUI SFTP Clients {.small-bullets}

 -   These let you transfer files to and from Wynton using a GUI
@ -232,9 +227,9 @@ echo "{local}$ scp alice@dt1.wynton.ucsf.edu:/path/to/local_file.tsv /destinatio
    -   Navigate to Preferences -\> Transfers -\> General
    -   change the Transfer Files setting "Use browser connection" instead of "Open Multiple connections"
 -   [FileZilla](https://filezilla-project.org/)
-    -   In the General tab, select ‘SFTP’ as the Protocol instead of ‘FTP’
-    -   For Logon Type, select ‘Interactive’ instead of ‘Ask for Password’
-    -   Under the Transfer Settings tab, you might need to click the ‘Limit number of simultaneous connections’ and make sure the ‘Maximum number of connections’ is set to 1
+    -   In the General tab, select 'SFTP' as the Protocol instead of 'FTP'
+    -   For Logon Type, select 'Interactive' instead of 'Ask for Password'
+    -   Under the Transfer Settings tab, you might need to click the 'Limit number of simultaneous connections' and make sure the 'Maximum number of connections' is set to 1

 ## Globus

@ -341,18 +336,18 @@ echo '[alice@dev1 ~]$ nextflow -v'

 # Containers

-## Motivation {.small-bullets .small-picture}
+## Motivation {.small-bullets}

 -   Compute heavy jobs (high RAM, multiple cores) should be run on compute nodes
 -   Containers allow us to make additional software available to the compute nodes
    -   Also allows the use of software that might be hard to install on Rocky 8 Linux
    -   Improves reproducibility

-![Compute Jobs](slide_materials/compute_job_workflow.png)
+![](slide_materials/compute_job_workflow.png){fig-alt="Compute Jobs workflow diagram" .nostretch fig-align="center" width=60%}

 ## Definitions {.small-bullets}

-   **Containers**: An isolated environment for running software that avoids conflicts with the host system. Containers are stored, shared and executed as **image files** with a .sif extension. 
+-   **Containers**: An isolated environment for running software that avoids conflicts with the host system. Containers are stored, shared and executed as **image files** with a .sif extension.
 -   **Images:** are built from definition files (or Dockerfiles) which are a set of instruction you specify for your environment.

 ## Apptainer {.small-bullets}
@ -390,8 +385,8 @@ echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif hi'
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo '    __  __     ____         _       __           __    __   __
   / / / /__  / / /___     | |     / /___  _____/ /___/ /  / /
-  / /_/ / _ \/ / / __ \    | | /| / / __ \/ ___/ / __  /  / / 
- / __  /  __/ / / /_/ /    | |/ |/ / /_/ / /  / / /_/ /  /_/  
+  / /_/ / _ \/ / / __ \    | | /| / / __ \/ ___/ / __  /  / /
+ / __  /  __/ / / /_/ /    | |/ |/ / /_/ / /  / / /_/ /  /_/
 /_/ /_/\___/_/_/\____/     |__/|__/\____/_/  /_/\__,_/  (_) '
 ```

@ -421,22 +416,23 @@ echo '[alice@dev1 ~]$ apptainer exec hello-world_1.0.sif cat /Dockerfile'

 ## Thank You!

-   Please take some time to fill out the workshop survey if you are not attending part 2:   
+-   Please take some time to fill out the workshop survey if you are not attending part 2:

-<https://www.surveymonkey.com/r/bioinfo-training>
+    <https://www.surveymonkey.com/r/bioinfo-training>

 ## Upcoming Data Science Training Program Workshops

-[Single Cell RNA-Seq Analysis](https://gladstone.org/index.php/events/single-cell-rna-seq-analysis-5)   
-March 27-March 28, 2025 9:00-12:00pm PDT   

-[Introduction to Linear Mixed Effects Models](https://gladstone.org/index.php/events/introduction-linear-mixed-effects-models-1)   
-April 3-April 4, 2025 1:00-3:00pm PDT   
+**Intermediate RNA-Seq Analysis Using R**   
+October 6, 2025 1:00-4:00pm PDT 

-[Introduction to scATAC-seq Data Analysis](https://gladstone.org/index.php/events/introduction-scatac-seq-data-analysis-0)   
-April 17-April 18, 2025 9:00am-12:00pm PDT   
+**Introduction to Pathway Analysis**   
+October 16, 2025 1:00-4:00pm PDT   

-[Introduction to Pathway Analysis](https://gladstone.org/index.php/events/introduction-pathway-analysis-3)   
-April 22, 2025 1:00-4:00pm PDT   

-[Complete Schedule](https://gladstone.org/events?series=189)
+**Statistics of Enrichment Analysis Methods **  
+October 20-October 21, 2025 1:00-3:00pm PDT   
+
+
+**Single Cell RNA-Seq Analysis**   
+October 27-October 28, 2025 9:00-4:00pm PDT   
--- a/working-on-wynton-hpc/Working_on_Wynton_Part_2.qmd
+++ b/working-on-wynton-hpc/Working_on_Wynton_Part_2.qmd
@ -1,38 +1,35 @@
 ---
 title: "Working on Wynton"
 subtitle: "Part 2"
-author: "Natalie Elphick"
-date: "March 25th, 2025"
-knit: (function(input, ...) {
-    rmarkdown::render(
-      input,
-      output_dir = "../docs"
-    )
-  })
-output:
-  revealjs::revealjs_presentation:
-    theme: simple
+author: "Natalie Gill"
+institute: "Gladstone Bioinformatics Core"
+date: "October 3, 2025"
+date-format: MMMM DD, YYYY
+format:
+  revealjs:
+    theme: wynton-theme.scss
    highlight: default
-    css: style.css
+    template-partials:
+      - title-slide.html
 ---

 ```{r, setup, include=FALSE}
 knitr::opts_chunk$set(comment = "")
 ```

-## 
+##

 <center>*Press the ? key for tips on navigating these slides*</center>

 ## Introductions
-Instructor:

-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**Natalie Elphick**   
+
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**Natalie Gill**   
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*Bioinformatician II*


 ## Target Audience
-   Prior experience with UNIX command-line 
+-   Prior experience with UNIX command-line



@ -42,7 +39,7 @@ Instructor:
 2.    Array Jobs
 3.    GPU Jobs
 4.    Running Pipelines
-5.    Jupyter Notebooks 
+5.    Jupyter Notebooks
 6.    RStudio Server
 7.    Advanced Tips and Tricks
 8.    How to get help
@ -50,11 +47,10 @@ Instructor:



-
 # Compute Jobs


-## Submission Script - Basics {.small-bullets .code-alt}
+## Submission Script - Basics {.small-bullets}

 -   [Download](https://www.dropbox.com/scl/fi/fzp33y1ojslw005q8epuz/simple_submission_script.sh?rlkey=xmg3lqec962y3i57a1bkriosx&dl=1) this example job submission script
 -   Read the full Wynton [job submission guide](https://wynton.ucsf.edu/hpc/scheduler/submit-jobs.html)
@ -71,11 +67,11 @@ rm submission.sh
 ## Submission Script - Apptainer

 -   Download the example job submission script that uses a container
-```{r,engine='bash', eval=FALSE, echo=TRUE}
-curl -s -L -o apptainer_submission_script.sh 'https://www.dropbox.com/scl/fi/zzl9fnfcoxu3pyrx5ffd1/apptainer_submission_script.sh?rlkey=w05e18ahw4hvbvaucac379za9&dl=1'
+```{r,engine='bash', eval=TRUE, echo=FALSE}
+echo "curl -s -L -o apptainer_submission_script.sh 'https://www.dropbox.com/scl/fi/zzl9fnfcoxu3pyrx5ffd1/apptainer_submission_script.sh?rlkey=w05e18ahw4hvbvaucac379za9&dl=1'"
 ```

-## Submission Script - Apptainer {.small-bullets .code-alt}
+## Submission Script - Apptainer {.small-bullets}

 -   Paths that the container needs read/write access to need to be mounted with APPTAINER_BINDPATH

@ -98,7 +94,7 @@ rm submission.sh
    -   **mpi_onehost**: for single-host parallel jobs based on MPI parallelization
    -   **mpi-8**: for multi-threaded multi-host jobs based on MPI parallelization

-## Example Parallel Job {.small-bullets .code-alt}
+## Example Parallel Job {.small-bullets}

 -   The simplest parallel environment on Wynton is **smp**, a single node with *n* cores
 -   [Download](https://www.dropbox.com/scl/fi/71xo0cioh266pj3uwcdps/smp_submission_script.sh?rlkey=kw7qaz8pip6jveqv317b5swqr&dl=1) this example smp job submission script
@ -122,7 +118,7 @@ echo 'curl -L -o array_job_example.zip https://www.dropbox.com/scl/fo/j0muxevls2

 ## Array Jobs {.small-bullets}

-   Unzip it 
+-   Unzip it
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo 'unzip array_job_example.zip -d array_job_example'
 ```
@ -154,10 +150,10 @@ Your job 714888 ("job1.sh") has been submitted'

 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo '[alice@dev1 ~]$ qstat
-job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
+job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
 -----------------------------------------------------------------------------------------------------------------
- 714888 0.06532 job1 alice     r     03/25/2024 19:54:18 member.q@msg-hmio1                 1        
- 714889 0.06532 job2 alice     r     03/25/2024 19:54:19 member.q@msg-hmio1                 1        
+ 714888 0.06532 job1 alice     r     03/25/2024 19:54:18 member.q@msg-hmio1                 1
+ 714889 0.06532 job2 alice     r     03/25/2024 19:54:19 member.q@msg-hmio1                 1
 '
 ```

@ -189,7 +185,7 @@ Any submitted job to compute nodes can also be run on development nodes.
 -   Scientific workflow system with a community maintained set of core bioinformatics [analysis pipelines](https://nf-co.re/)
 -   The most commonly used one is the [RNA-seq pipeline](https://nf-co.re/rnaseq/3.14.0)

-![RNA-seq](slide_materials/nf-core-rnaseq_metro_map_grey.png)
+![](slide_materials/nf-core-rnaseq_metro_map_grey.png){fig-alt="RNA-seq workflow diagram showing nf-core pipeline steps" .nostretch fig-align="center" width=70%}


 ## Example - RNA-seq Pipeline {.small-bullets}
@ -208,8 +204,7 @@ Any submitted job to compute nodes can also be run on development nodes.



-
-# Jupyter Notebooks 
+# Jupyter Notebooks

 ## Installing Jupyter Notebooks
 -   The preferred way to install and use [Jupyter notebooks](https://wynton.ucsf.edu/hpc/howto/jupyter.html) on Wynton is though pip, not conda
@ -234,7 +229,7 @@ echo '[alice@dev1 ~]$ module load CBI port4me
 Note the port number returned by port4me, you will need this later.


-## Running Jupyter Notebooks - Step 2 {.code-small}
+## Running Jupyter Notebooks - Step 2
 -   Launch Jupyter notebook using the port numer from step 1
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo '[alice@dev1]$ jupyter notebook --no-browser --port 47467
@ -287,7 +282,7 @@ The notebook should now be available at the URL from step 2
    -   One to connect to it


-## RStudio Server - Step 1 {.code-small}
+## RStudio Server - Step 1

 -   Launch your own RStudio Server instance
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
@ -379,7 +374,7 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
 -   Network latency becomes extremely important for all metadata requests
 -   Certain input/output patterns can be problematic

-## BeeGFS - I/O patterns 
+## BeeGFS - I/O patterns

 -   Anything that requires lots of metadata operations can feel slow
    -   e.g: lots of writes to the same directory and lots of file lookups and directory searches (**conda**)
@ -393,7 +388,7 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
 -   Don't include anything in **/wynton** in your default LD_LIBRARY_PATH
 -   If using conda, putting the conda application inside a Apptainer (formerly singularity) container will result in better performance

-## Custom Containers
+# Custom Containers

 ## Motivation {.small-bullets .small-picture}

@ -402,7 +397,7 @@ For any bioinformatics specific questions feel free to reach out to the Gladston
    -   Also allows the use of software that might be hard to install on Rocky 8 Linux
    -   Improves reproducibility

-![Compute Jobs](slide_materials/compute_job_workflow.png)
+![](slide_materials/compute_job_workflow.png){fig-alt="Compute Jobs workflow diagram" .nostretch fig-align="center" width=60%}



@ -429,7 +424,7 @@ echo 'docker build .'

 See the [Dockerfile documentation](https://docs.docker.com/reference/dockerfile/) for a full list of instructions

-## Example Dockerfile {.code-alt}
+## Example Dockerfile

 -   Click [here](https://www.dropbox.com/scl/fi/mdbefp3h8ahdvxtgjypqo/Dockerfile?rlkey=7d4zd9ge1m3wwszlfy78712ky&dl=1) to download the example Dockerfile
 -   Open in your preffered text editor
@ -447,7 +442,7 @@ rm Dockerfile
    -   It requires a lot of RAM
 -   On macOS, make sure you have the Docker Desktop App running
 -   We can provide an additional argument to the **build** command, -t, to set the name of the docker image
-      -   We can add version tags after the name using ":" 
+      -   We can add version tags after the name using ":"
 ```{r, engine='bash', eval=TRUE, results='markup',comment=NA, highlight=TRUE, echo=FALSE}
 echo "docker build -t docker_hub_user/seurat-harmony:1.0 ."
 ```
@ -483,25 +478,23 @@ echo "[alice@dev1 ~]$ apptainer pull docker://docker_hub_user/seurat-harmony:1.0
 ## Thank You!


-   Please take some time to fill out the workshop survey:   
+-   Please take some time to fill out the workshop survey:

 <https://www.surveymonkey.com/r/bioinfo-training>

 ## Upcoming Data Science Training Program Workshops

-[Single Cell RNA-Seq Analysis](https://gladstone.org/index.php/events/single-cell-rna-seq-analysis-5)   
-March 27-March 28, 2025 9:00-12:00pm PDT   

-[Introduction to Linear Mixed Effects Models](https://gladstone.org/index.php/events/introduction-linear-mixed-effects-models-1)   
-April 3-April 4, 2025 1:00-3:00pm PDT   
+**Intermediate RNA-Seq Analysis Using R**   
+October 6, 2025 1:00-4:00pm PDT 

-[Introduction to scATAC-seq Data Analysis](https://gladstone.org/index.php/events/introduction-scatac-seq-data-analysis-0)   
-April 17-April 18, 2025 9:00am-12:00pm PDT   
-
-[Introduction to Pathway Analysis](https://gladstone.org/index.php/events/introduction-pathway-analysis-3)   
-April 22, 2025 1:00-4:00pm PDT   
-
-[Complete Schedule](https://gladstone.org/events?series=189)
+**Introduction to Pathway Analysis**   
+October 16, 2025 1:00-4:00pm PDT   


+**Statistics of Enrichment Analysis Methods **  
+October 20-October 21, 2025 1:00-3:00pm PDT   

+
+**Single Cell RNA-Seq Analysis**   
+October 27-October 28, 2025 9:00-4:00pm PDT   
--- a/working-on-wynton-hpc/render_slides.sh
+++ b/working-on-wynton-hpc/render_slides.sh
@ -0,0 +1,78 @@
+#!/bin/bash
+
+# Wrapper script for rendering Quarto slides to match R Markdown output behavior
+# This script renders both Working on Wynton presentations to the ../docs directory
+
+# Set script to exit on any error
+set -e
+
+echo "🚀 Starting Quarto slide rendering..."
+
+# Create docs directory if it doesn't exist
+DOCS_DIR="../docs/Working_on_Wynton"
+if [ ! -d "$DOCS_DIR" ]; then
+    echo "📁 Creating output directory: $DOCS_DIR"
+    mkdir -p "$DOCS_DIR"
+fi
+
+# Copy image assets to docs directory
+echo "🖼️  Copying image assets to $DOCS_DIR..."
+
+# Copy slide materials directory
+if [ -d "slide_materials" ]; then
+    cp -r slide_materials "$DOCS_DIR/"
+    echo "📁 Copied slide_materials to $DOCS_DIR"
+fi
+
+# Copy logo image
+if [ -f "gladstone_logo_slide.png" ]; then
+    cp gladstone_logo_slide.png "$DOCS_DIR/"
+    echo "🖼️  Copied gladstone_logo_slide.png to $DOCS_DIR"
+fi
+
+# Function to render a single slide presentation
+render_slide() {
+    local slide_file="$1"
+    local slide_name=$(basename "$slide_file" .qmd)
+
+    echo "🔧 Rendering $slide_file..."
+
+    # Render the Quarto presentation in current directory
+    quarto render "$slide_file" --to revealjs
+
+    if [ $? -eq 0 ]; then
+        echo "✅ Successfully rendered: ${slide_name}.html"
+
+        # Move the HTML file to docs directory
+        if [ -f "${slide_name}.html" ]; then
+            mv "${slide_name}.html" "$DOCS_DIR/"
+            echo "📁 Moved ${slide_name}.html to $DOCS_DIR"
+        fi
+
+        # Sync the supporting files directory if it exists
+        if [ -d "${slide_name}_files" ]; then
+            rsync -av "${slide_name}_files/" "$DOCS_DIR/${slide_name}_files/"
+            rm -rf "${slide_name}_files"
+            echo "📁 Synced ${slide_name}_files to $DOCS_DIR"
+        fi
+    else
+        echo "❌ Failed to render: $slide_file"
+        exit 1
+    fi
+}
+
+# Render both presentations
+render_slide "Working_on_Wynton_Part_1.qmd"
+render_slide "Working_on_Wynton_Part_2.qmd"
+
+
+echo ""
+echo "🎉 All slides rendered successfully!"
+echo "📍 Output location: $DOCS_DIR"
+echo ""
+echo "📄 Generated files:"
+ls -la "$DOCS_DIR"/*.html 2>/dev/null || echo "   No HTML files found"
+echo ""
+echo "🌐 To view the slides, open the HTML files in a web browser:"
+echo "   - ${DOCS_DIR}/Working_on_Wynton_Part_1.html"
+echo "   - ${DOCS_DIR}/Working_on_Wynton_Part_2.html"
--- a/working-on-wynton-hpc/renv.lock
+++ b/working-on-wynton-hpc/renv.lock
@ -1,361 +0,0 @@
-{
-  "R": {
-    "Version": "4.4.1",
-    "Repositories": [
-      {
-        "Name": "CRAN",
-        "URL": "https://packagemanager.posit.co/cran/latest"
-      }
-    ]
-  },
-  "Packages": {
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.6.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "lifecycle",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
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--- a/working-on-wynton-hpc/renv/.gitignore
+++ b/working-on-wynton-hpc/renv/.gitignore
@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/
--- a/working-on-wynton-hpc/renv/activate.R
+++ b/working-on-wynton-hpc/renv/activate.R
--- a/working-on-wynton-hpc/renv/settings.json
+++ b/working-on-wynton-hpc/renv/settings.json
@ -1,19 +0,0 @@
-{
-  "bioconductor.version": null,
-  "external.libraries": [],
-  "ignored.packages": [],
-  "package.dependency.fields": [
-    "Imports",
-    "Depends",
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-  "r.version": null,
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-  "vcs.ignore.library": true,
-  "vcs.ignore.local": true,
-  "vcs.manage.ignores": true
-}
--- a/working-on-wynton-hpc/slide_materials/Gladstone_Wynton_Docs.pdf
+++ b/working-on-wynton-hpc/slide_materials/Gladstone_Wynton_Docs.pdf
--- a/working-on-wynton-hpc/slide_materials/gladstone_logo_slide.png
+++ b/working-on-wynton-hpc/slide_materials/gladstone_logo_slide.png
--- a/working-on-wynton-hpc/slide_materials/status-chart.png
+++ b/working-on-wynton-hpc/slide_materials/status-chart.png
--- a/working-on-wynton-hpc/style.css
+++ b/working-on-wynton-hpc/style.css
@ -1,184 +0,0 @@
-
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-.bottom-message {
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-    font-style: italic !important;
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-
-.reveal code {
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-}
-
-.code-small code {
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-.reveal code::selection {
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-.reveal pre code.output {
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-.reveal h3 {
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-.reveal .slides>section:first-child h2 {
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-.reveal p {
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-.reveal ul ul {
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-.reveal ol {
-    display: block;
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-
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-.reveal img {
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-    border: none !important;
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-small {
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-/* Create a custom class for the small bullets, increase the spacing between list items */
-.small-bullets ul {
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-.small-list ol {
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-.reveal li {
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-
-
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-.small-picture img{
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-.reveal a {
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-.reveal a:hover {
-    color: #9c0366 !important;
-}
--- a/working-on-wynton-hpc/title-slide.html
+++ b/working-on-wynton-hpc/title-slide.html
@ -0,0 +1,28 @@
+<!-- Logo slide -->
+<section class="slide level2" data-background-image="slide_materials/gladstone_logo_slide.png" data-background-size="contain">
+</section>
+
+<!-- Title slide -->
+<section class="quarto-title-block">
+  <h1 class="title">$title$</h1>
+$if(subtitle)$
+  <p class="subtitle">$subtitle$</p>
+$endif$
+$if(author)$
+  <div class="quarto-title-authors">
+    <div class="quarto-title-author">
+      <div class="quarto-title-author-name">$author$</div>
+$if(institute)$
+      <div class="quarto-title-affiliation">$institute$</div>
+$endif$
+    </div>
+  </div>
+$endif$
+$if(date)$
+  <div class="quarto-title-meta">
+    <div class="quarto-title-meta-contents">
+      <p class="date">$date$</p>
+    </div>
+  </div>
+$endif$
+</section>
--- a/working-on-wynton-hpc/working-on-wynton-hpc.Rproj
+++ b/working-on-wynton-hpc/working-on-wynton-hpc.Rproj
@ -1,14 +0,0 @@
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-ProjectId: 34071a3d-003e-4263-bd00-68a4cf53c544
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-
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-NumSpacesForTab: 2
-Encoding: UTF-8
-
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-LaTeX: pdfLaTeX
--- a/working-on-wynton-hpc/wynton-theme.scss
+++ b/working-on-wynton-hpc/wynton-theme.scss
@ -0,0 +1,214 @@
+/**
+ * Wynton HPC Training Theme for reveal.js presentations
+ *
+ * Adapted from the original style.css for the Working on Wynton training materials
+ * Converted to SCSS format for better maintainability and theming capabilities
+ */
+
+/*-- scss:defaults --*/
+
+// Custom color palette
+$primary-color: #9c0366;
+$secondary-color: #BB3E03;
+$link-color: #0c74dc;
+$link-hover-color: #9c0366;
+$code-bg: #333333;
+$code-block-bg: #333333;
+$code-color: white;
+$code-block-font-size: 0.8em;
+
+// Typography
+$font-family-sans-serif: "Helvetica", sans-serif !default;
+$font-family-monospace: "Menlo", sans-serif !default;
+
+// Override Quarto reveal.js defaults
+$presentation-heading-font: $font-family-sans-serif !default;
+$presentation-heading-color: $primary-color !default;
+$presentation-heading-text-transform: none !default;
+$presentation-heading-text-shadow: none !default;
+$link-color-default: $link-color !default;
+$presentation-list-bullet-color: $secondary-color !default;
+
+/*-- scss:rules --*/
+
+// Define CSS custom properties for dynamic theming
+:root {
+  --r-list-bullet-color: #{$presentation-list-bullet-color};
+}
+
+// Font family overrides
+pre, code, kbd, samp {
+  font-family: $font-family-monospace;
+}
+
+.reveal {
+  // Typography
+  p, li, h1, h2, h3, h4, h5, h6 {
+    font-family: $font-family-sans-serif;
+  }
+
+  // Heading styles
+  h1 {
+    font-weight: bold !important;
+    color: $primary-color;
+    font-size: 2.0em;
+  }
+
+  h2 {
+    font-weight: bold !important;
+    color: $primary-color;
+    font-size: 1.3em;
+  }
+
+  h3 {
+    color: black;
+    font-size: 0.7em;
+  }
+
+  // Special handling for first slide
+  .slides > section:first-child {
+    h1 {
+      font-weight: bold !important;
+      color: $primary-color;
+    }
+
+    h2 {
+      color: black;
+      color: $primary-color;
+      font-weight: normal !important;
+    }
+  }
+
+  // Custom colored list bullets
+  ul,
+  ol {
+    li::marker {
+      color: var(--r-list-bullet-color);
+    }
+  }
+}
+
+// Slide content styling - using .reveal .slide prefix for best practices
+.reveal .slide {
+  // Ensure slide titles remain centered
+  h1, h2 {
+    text-align: center;
+  }
+
+  // Paragraph styling for slide content only (not titles)
+  p:not(.subtitle) {
+    text-align: left;
+    margin-left: 20px;
+  }
+
+  // List styling for slide content only
+  ul {
+    display: block;
+    margin-left: 75px;
+    margin-right: 50px;
+
+    ul {
+      font-size: 0.75em;
+      margin-bottom: 5px;
+    }
+  }
+
+  ol {
+    display: block;
+    margin-bottom: 20px;
+    margin-left: 75px;
+    margin-right: 50px;
+  }
+
+  li {
+    margin-bottom: 10px;
+  }
+
+  // Custom colored list bullets for slide content
+  ul,
+  ol {
+    li::marker {
+      color: var(--r-list-bullet-color);
+    }
+  }
+}
+
+// Code styling - applies to all reveal content with higher specificity
+.reveal pre,
+.reveal code {
+  background-color: $code-block-bg !important;
+  color: white !important;
+  font-family: $font-family-monospace !important;
+  font-size: $code-block-font-size !important;
+  line-height: 1.2 !important;
+}
+
+.reveal pre code {
+  background-color: transparent !important;  // inherit from pre
+  color: inherit !important;  // inherit from pre
+  text-align: left !important;
+  white-space: pre !important;
+  overflow-x: auto !important;
+}
+
+
+// Image and link styling - applies to all reveal content
+.reveal {
+  img {
+    max-width: 70%;
+    border: none;
+    box-shadow: none;
+    display: block;
+    margin: 0 auto;
+  }
+
+  a {
+    color: $link-color;
+
+    &:hover {
+      color: $link-hover-color;
+    }
+  }
+}
+
+// Custom utility classes
+.bottom-message {
+  font-size: 0.8em !important;
+  font-style: italic !important;
+  text-align: center;
+  position: relative;
+  bottom: 0 !important;
+  left: 0;
+  right: 0;
+}
+
+
+// Size utility classes
+small {
+  font-size: 70%;
+}
+
+.small-bullets ul {
+  font-size: 85%;
+}
+
+.less-small-bullets ul {
+  font-size: 80%;
+}
+
+.small-list ol {
+  font-size: 80%;
+}
+
+// Image size classes
+.big-picture img {
+  max-width: 95%;
+}
+
+.small-picture img {
+  max-width: 65%;
+}
+
+.smaller-picture img {
+  max-width: 60%;
+}