From 56bed77b64ce2b9743201bc0c236672058026ce7 Mon Sep 17 00:00:00 2001
From: Roy Francis <roymathewfrancis@gmail.com>
Date: Thu, 6 Mar 2025 17:24:09 +0100
Subject: [PATCH] Updated docker image. Updated quarto, added new R pkgs for
 updated lab.

---
 README.md  | 10 +++++-----
 dockerfile | 16 ++++++++++------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index c17f1360..570c79a7 100644
--- a/README.md
+++ b/README.md
@@ -30,17 +30,17 @@ as the first thing, so that old rendered files are not overwritten.
 
 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.
 
-:exclamation: **Note:** Image size: 4.86GB.
+:exclamation: **Note:** Image size: 5.4GB.
 
 Clone the repo if not already done. Make sure you are standing in the repo directory.
 
-To build the complete site,
+To render the complete site,
 
 ```
 docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest
 ```
 
-To build a single file (for example `index.qmd`),
+To render a single file (for example `index.qmd`),
 
 ```
 docker run --platform linux/amd64 --rm -u 1000:1000 -v ${PWD}:/qmd ghcr.io/nbisweden/workshop-ngsintro:latest quarto render index.qmd
@@ -69,11 +69,11 @@ Go to [http://localhost:8800/](http://localhost:8800/) or [http://0.0.0.0:8800](
 
 ```bash
 # build container
-docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.4.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
+docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.5.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
 
 # push to ghcr
 # docker login ghcr.io
-docker push ghcr.io/nbisweden/workshop-ngsintro:2.4.0
+docker push ghcr.io/nbisweden/workshop-ngsintro:2.5.0
 docker push ghcr.io/nbisweden/workshop-ngsintro:latest
 
 # run container in the root of the repo
diff --git a/dockerfile b/dockerfile
index 7fef06f9..e3ea2dec 100644
--- a/dockerfile
+++ b/dockerfile
@@ -1,11 +1,11 @@
 # DOCKER FILE FOR WORKSHOP-NGSINTRO
 # 2025 Roy Francis
 
-FROM rocker/verse:4.4
+FROM ghcr.io/rocker-org/verse:4.4.3
 LABEL Description="Docker image for NBIS workshop"
 LABEL Maintainer="roy.francis@nbis.se"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-ngsintro"
-#ARG QUARTO_VERSION="1.6.40"
+ARG QUARTO_VERSION="1.6.42"
 
 RUN apt-get update -y \
   && apt-get clean \
@@ -19,9 +19,9 @@ RUN apt-get update -y \
   #&& 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 \
+  && 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 \
@@ -38,5 +38,9 @@ WORKDIR /qmd
 #ENV XDG_DATA_HOME=/tmp/quarto_data_home
 CMD ["quarto", "render"]
 
-# docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.3.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
+# local build
+# docker build --platform linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.5.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest .
+# multiplatform build and push to repository (doesn't work)
+# docker buildx build --platform=linux/arm64,linux/amd64 -t ghcr.io/nbisweden/workshop-ngsintro:2.5.0 -t ghcr.io/nbisweden/workshop-ngsintro:latest --push -f Dockerfile .
+# build singularity
 # 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