Updated docker image to quarto 1.4

.github/workflows/docker.yml

@@ -7,7 +7,7 @@ on:
 env:
   REGISTRY: ghcr.io
   ORG: nbisweden
-  IMAGE: workshop-ngsintro/workshop-ngsintro:latest
+  IMAGE: workshop-ngsintro:latest
 
 jobs:
   quarto-render-job:

Dockerfile

@@ -0,0 +1,36 @@
+# DOCKER FILE FOR WORKSHOP-NGSINTRO
+# 2024 Roy Francis
+
+FROM rocker/verse:4.2.3
+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"
+
+RUN apt-get update -y \
+  && 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");' \
+  && rm -rf /var/lib/apt/lists/* \
+  && 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"));'
+WORKDIR /qmd
+#ENV XDG_CACHE_HOME=/tmp/quarto_cache_home
+#ENV XDG_DATA_HOME=/tmp/quarto_data_home
+CMD quarto render
+

README.md

@@ -36,22 +36,40 @@ Clone the repo if not already done. Make sure you are standing in the repo direc
 To build the complete site,
 
 ```
-docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro/workshop-ngsintro
+docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro
 ```
 
 To build a single file (for example `index.qmd`),
 
 ```
-docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro/workshop-ngsintro quarto render index.qmd
+docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro quarto render index.qmd
 ```
 
 :exclamation: Output files are for local preview only. Do not push any rendered .html files or intermediates.
 
 ## Repo organisation
 
-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 content in master. Changes pushed to the *master* branch is automatically rendered to the *gh-pages* branch.
+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.
 
-:exclamation: Every push rebuilds the whole website using a docker image. Build takes about 4-5 mins.
+:exclamation: Every push rebuilds the whole website using a pre-built docker image.
+
+This repo is loosely based on the quarto template [specky](https://github.com/royfrancis/specky).
+
+## Building 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 .
+
+# push to ghcr
+# docker login ghcr.io
+docker push ghcr.io/nbisweden/workshop-ngsintro:2.3.0
+docker push ghcr.io/nbisweden/workshop-ngsintro:latest
+
+# run container in the root of the repo
+docker run --rm --platform linux/amd64 -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest
+docker run --rm --platform linux/amd64 -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest quarto render index.qmd
+```
 
 ## Test scripts