Merge branch 'roy'

Dockerfile

@@ -1,36 +1,42 @@
 # DOCKER FILE FOR WORKSHOP-NGSINTRO
-# 2024 Roy Francis
+# 2025 Roy Francis
 
-FROM rocker/verse:4.2.3
+FROM rocker/verse:4.4
 LABEL Description="Docker image for NBIS workshop"
 LABEL Maintainer="[email protected]"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-ngsintro"
-ARG QUARTO_VERSION="1.4.549"
+#ARG QUARTO_VERSION="1.6.40"
 
 RUN apt-get update -y \
+  && apt-get clean \
   && apt-get install --no-install-recommends -y \
   libxml2-dev \
   libssl-dev \
   libcurl4-openssl-dev \
   libudunits2-dev \
-  libopenblas-base \
   libgdal-dev \
   curl \
-  && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
-  && apt-get install -y ./google-chrome-stable_current_amd64.deb \
-  && rm -rf ./google-chrome-stable_current_amd64.deb \
-  && curl -o quarto-linux-amd64.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb \
-  && apt-get install -y ./quarto-linux-amd64.deb \
-  && rm -rf ./quarto-linux-amd64.deb \
-  && Rscript -e 'install.packages(c("remotes","fontawesome","here","htmlTable","leaflet","readxl","writexl"),repos = "http://cran.us.r-project.org");' \
+  #&& wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
+  #&& apt-get install -y ./google-chrome-stable_current_amd64.deb \
+  #&& rm -rf ./google-chrome-stable_current_amd64.deb \
+  #&& curl -o quarto-linux-amd64.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb \
+  #&& apt-get install -y ./quarto-linux-amd64.deb \
+  #&& rm -rf ./quarto-linux-amd64.deb \
   && rm -rf /var/lib/apt/lists/* \
+  && install2.r --error --skipinstalled remotes fontawesome here htmlTable leaflet readxl writexl \
+  && rm -rf /tmp/downloaded_packages \
   && mkdir /qmd /.cache \
   && chmod 777 /qmd /.cache
 
-## Required when editing rnaseq
-## RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","goseq","GO.db","org.Mm.eg.db","reactome.db"));'
+USER rstudio
+
+## Required when editing rnaseq lab
+RUN Rscript -e 'install.packages(c("pheatmap","ggrepel"),repos = "http://cran.us.r-project.org"); BiocManager::install(c("DESeq2", "edgeR", "org.Mm.eg.db", "clusterProfiler"));'
+
 WORKDIR /qmd
 #ENV XDG_CACHE_HOME=/tmp/quarto_cache_home
 #ENV XDG_DATA_HOME=/tmp/quarto_data_home
-CMD quarto render
+CMD ["quarto", "render"]
 
+# docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.3.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
+# docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):/work kaczmarj/apptainer build ngsintro.sif docker://ghcr.io/nbisweden/workshop-ngsintro:latest

README.md

@@ -25,6 +25,7 @@ as the first thing, so that old rendered files are not overwritten.
 
 :exclamation: Do not push any rendered .html files or intermediates.
 
+## Docker
 ### Local build/preview using Docker
 
 You can preview changes and build the whole website locally without a local installation of R or dependency packages by using the pre-built Docker image.
@@ -47,46 +48,46 @@ docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisw
 
 :exclamation: Output files are for local preview only. Do not push any rendered .html files or intermediates.
 
-## Convert HTML slides to PDF
+### Convert HTML slides to PDF
 
 ```
 docker run --platform=linux/amd64 -v $PWD:/work astefanutti/decktape https://nbisweden.github.io/workshop-ngsintro/2403/topics/rnaseq/slide_rnaseq.html /work/slide_rnaseq.pdf
 ```
 
-## Repo organisation
+### Serving and automatic rendering
 
-The source material is located on the *master* branch (default). The rendered material is located on the *gh-pages* branch. One only needs to update source materials in *master*. Changes pushed to the *master* branch is automatically rendered to the *gh-pages* branch using github actions.
+You can use `quarto preview` to serve the site, and handle automatic rebuilding of pages when any `.qmd` file is changed.
 
-:exclamation: Every push rebuilds the whole website using a pre-built docker image.
+```bash
+# serve the site
+docker run --rm -it --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd -p 8800:8800  ghcr.io/nbisweden/workshop-ngsintro:latest quarto preview --port 8800 --host 0.0.0.0
+```
 
-This repo is loosely based on the quarto template [specky](https://github.com/royfrancis/specky).
+Go to [http://localhost:8800/](http://localhost:8800/) or [http://0.0.0.0:8800](http://0.0.0.0:8800) in your browser.
 
-## Building docker container
+### Building your own docker container
 
 ```bash
 # build container
-docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.3.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
+docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.4.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
 
 # push to ghcr
 # docker login ghcr.io
-docker push ghcr.io/nbisweden/workshop-ngsintro:2.3.0
+docker push ghcr.io/nbisweden/workshop-ngsintro:2.4.0
 docker push ghcr.io/nbisweden/workshop-ngsintro:latest
 
 # run container in the root of the repo
 docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest
 docker run --rm --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest quarto render index.qmd
 ```
 
-## Serving and automatic rendering
+## Repo organisation
 
-You can use `quarto preview` to serve the site, and handle automatic rebuilding of pages when any `.qmd` file is changed.
+The source material is located on the *master* branch (default). The rendered material is located on the *gh-pages* branch. One only needs to update source materials in *master*. Changes pushed to the *master* branch is automatically rendered to the *gh-pages* branch using github actions.
 
-```bash
-# serve the site
-docker run --rm -it --platform linux/amd64 -u $(id -u):$(id -g) -v ${PWD}:/qmd -p 8800:8800  ghcr.io/nbisweden/workshop-ngsintro:latest quarto preview --port 8800 --host 0.0.0.0
-```
+:exclamation: Every push rebuilds the whole website using a pre-built docker image.
 
-Go to [http://localhost:8800/](http://localhost:8800/) or [http://0.0.0.0:8800](http://0.0.0.0:8800) in your browser.
+This repo is loosely based on the quarto template [specky](https://github.com/royfrancis/specky).
 
 ## Test scripts
 
@@ -98,4 +99,4 @@ The contents of these scripts should use identical steps and tools as the studen
 
 ---
 
-**2024** • NBIS • SciLifeLab
+**2025** • NBIS • SciLifeLab

_quarto.yml

@@ -115,6 +115,7 @@ execute:
 
 filters:
   - assets/custom.lua
+  - assets/fold-results.lua
   - reveal-logo
 
 # used site-wide
@@ -138,8 +139,9 @@ id_slurm_res_wed: "edu25-03-26"
 id_slurm_res_thu: "edu25-03-27"
 id_slurm_res_fri: "edu25-03-28"
 
-# location options are linkoping, lund, umea, uppsala or online. For rendering the info page.
-# one or more separated by commas or semicolon. online doesn't display any location info.
+# location is used to render the info page
+# location options are linkoping, lund, umea, stockholm, uppsala or online
+# one or more separated by commas or semicolon.
 location: online
 assistants:
  - "AJ: Anna Johansson"

assets/_child-info.qmd

@@ -1,10 +1,12 @@
 ```{r}
 #| echo: false
+icons <- awesomeIcons(icon = dfr2$marker_icon, markerColor = dfr2$marker_color, iconColor = "#FFFFFF", library = "fa")
+
 htmltools::div(
   style = "margin-bottom:1em;",
   htmltools::tagList(leaflet(height = 450, width = "auto", elementId = paste0("leaflet-", p)) %>%
     addTiles(urlTemplate = "http://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png") %>%
     addAwesomeMarkers(lat = dfr2$lat, lng = dfr2$lon, label = dfr2$label, popup = dfr2$popup, icon = icons) %>%
     setView(lat = dfr2$lat[1], lng = dfr2$lon[1], zoom = 13))
 )
-```
+```

assets/css/home.css

@@ -10,11 +10,11 @@ body {
 }
 
 .navbar {
-    background-color: transparent !important;
+  background-color: transparent !important;
 }
 
 .nav-footer {
-    background-color: transparent !important;
+  background-color: transparent !important;
 }
 
 .home-container {

assets/css/slides.scss

@@ -65,6 +65,11 @@ $presentation-h6-font-size: 1em;
   margin-bottom: 0.5em;
 }
 
+.reveal .code-with-filename-file pre {
+  background-color: transparent;
+  font-size: 80% !important;
+}
+
 .reveal pre,
 .reveal code {
   border-radius: 6px;
@@ -118,6 +123,26 @@ $presentation-h6-font-size: 1em;
   text-align: right;
 }
 
+/* vertical alignment */
+
+.reveal .v-center {
+  display: grid;
+  align-items: center;
+  height: 90%;
+}
+
+.reveal .v-top {
+  display: grid;
+  align-items: start;
+  height: 90%;
+}
+
+.reveal .v-bottom {
+  display: grid;
+  align-items: end;
+  height: 90%;
+}
+
 /* lists */
 
 .reveal .slide ul,

assets/css/styles.scss

@@ -15,6 +15,7 @@ $code-color: #496985;
 $code-block-bg: WhiteSmoke;
 $font-family-sans-serif: 'Nunito', 'Source Sans Pro', 'Helvetica', 'sans-serif' ;
 $font-family-monospace: 'Fira Mono', 'Ubuntu Mono', 'Liberation Mono', 'Lucida Console', 'Courier', 'monospace';
+$mermaid-font-family: 'Nunito', 'Source Sans Pro', 'Helvetica', 'sans-serif' ;
 $font-size-root: 18px;
 $code-font-size: 14px;
 /* major second scale */

assets/fold-results.lua

@@ -0,0 +1,20 @@
+-- Fold output from code chunks
+-- In code chunk, add #| attr.output: '.details summary="Output"'
+-- Only works for knitr chunks
+-- https://gist.github.com/atusy/f2b5b992e45c68ab6823499f2339c6e6
+
+function CodeBlock(elem)
+  if elem.classes and elem.classes:find("details") then
+    local summary = "Code"
+    if elem.attributes.summary then
+      summary = elem.attributes.summary
+    end
+    return{
+      pandoc.RawBlock(
+        "html", "<details><summary>" .. summary .. "</summary>"
+      ),
+      elem,
+      pandoc.RawBlock("html", "</details>")
+    }
+  end
+end

home_info.qmd

@@ -12,11 +12,45 @@ format: html
 library(yaml)
 library(here)
 library(leaflet)
-library(readxl)
+
+#' Get location data from YAML into a list and data.frame
+#' @param y YAML data
+#' @param loc Name of location
+#' @return List with description and data.frame with map data
+#'
+get_info <- function(y, loc) {
+  loc <- tolower(loc)
+
+  if (loc %in% names(y)) {
+    info <- y[[loc]]
+    if (!is.null(info$description)) {
+      d <- info$description
+    } else {
+      d <- NULL
+    }
+    if (!is.null(info$map)) {
+      m <- do.call(rbind, lapply(info$map, function(x){
+        required_fields <- c("label", "marker_icon", "marker_color", "lat", "lon", "popup")
+        missing_fields <- setdiff(required_fields, names(x))
+        
+        if (length(missing_fields) > 0) {
+          stop(paste("Missing fields:", paste(missing_fields, collapse = ", ")))
+        }
+        as.data.frame(x)
+      }))
+    } else {
+      m <- NULL
+    }
+    return(list(description = d, map = m))
+  } else {
+    message(paste0("Location ", loc, " not found in the data"))
+    return(NULL)
+  }
+}
 
 # set location in _quarto.yml
-loc <- sapply(unlist(strsplit(yaml::read_yaml(here("_quarto.yml"))$location,";|,")),trimws)
-dfr <- readxl::read_xlsx("info.xlsx")
+loc <- sapply(unlist(strsplit(yaml::read_yaml(here("_quarto.yml"))$location, ";|,")), trimws)
+l <- yaml::yaml.load_file(here("info.yml"))
 ```
 
 ## Location
@@ -25,25 +59,27 @@ dfr <- readxl::read_xlsx("info.xlsx")
 cat("\n::: {.panel-tabset}\n")
 
 for (i in seq_along(loc)) {
-    p <- loc[i]
-    cat(paste0("\n### ", tools::toTitleCase(p), "\n"))
+  p <- loc[i]
+  cat(paste0("\n### ", tools::toTitleCase(p), "\n"))
 
-    if(p %in% dfr$location){
-      dfr1 <- dfr[dfr$location %in% p, , drop = FALSE]
-      dfr1$address <- gsub(";|; ", "<br>", dfr1$address)
+  idata <- get_info(l, p)
+  if (!is.null(idata)) {
+    if (!is.null(idata$map)) {
+      dfr1 <- idata$map
       dfr1$popup <- gsub(";|; ", "<br>", dfr1$popup)
       dfr2 <- dfr1[complete.cases(dfr1$lat, dfr1$lon), ]
-      icons <- awesomeIcons(icon = dfr2$marker_icon, markerColor = dfr2$marker_colour, iconColor = "#FFFFFF", library = "fa")
-      if(p != "online") {
-        cat(knitr::knit_child(input = "assets/_child-info.qmd", envir = environment(), quiet = TRUE))
-        cat("\n")
-        cat("\n", dfr1$address[1], "\n")
-      }
-      cat("\n", dfr1$description[1])
-    }else{
-      cat("No additional information is provided.")
+      
+      cat(knitr::knit_child(input = "assets/_child-info.qmd", envir = environment(), quiet = TRUE))
+      cat("\n")
+    }
+
+    if (!is.null(idata$description)) {
+      cat("\n", idata$description)
     }
-    cat("\n")
+  } else {
+    cat("No additional information is provided.")
+  }
+  cat("\n")
 }
 
 cat(":::\n")