Updated

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