feat: the great rewrite

Author: eseiler

.gitignore

@@ -0,0 +1,2 @@
+/local
+report.knit.md

database/IP2LOCATION-LITE-DB5.BIN

@@ -1,13 +1,20 @@
 # syntax=docker/dockerfile:1
 
-FROM debian:trixie-slim
+FROM jenkins/agent:latest-trixie
 
 ENV DEBIAN_FRONTEND=noninteractive
 ENV GNUMAKEFLAGS="-j2 --no-print-directory --output-sync=target"
 ENV MAKEFLAGS="-j2 --no-print-directory --output-sync=target"
 ENV RSTUDIO_PANDOC=/usr/bin
 ENV TZ=Europe/Berlin
 
+USER root
+
+# Overwrite TZ from jenkins image.
+RUN ln -snf /usr/share/zoneinfo/"${TZ}" /etc/localtime && \
+    echo "${TZ}" > /etc/timezone && \
+    dpkg-reconfigure tzdata
+
 SHELL ["/bin/bash", "-Eeuxo", "pipefail", "-c"]
 
 COPY docker_scripts /docker_scripts
@@ -17,4 +24,13 @@ ENV EXTRA_CXXFLAGS=-w
 COPY config/Makevars /root/.R/Makevars
 
 RUN /docker_scripts/install_apt_packages.sh
+
+COPY --from=config r-requirements.txt /docker_scripts/
 RUN /docker_scripts/install_R_packages.R
+
+COPY --from=config requirements.txt /docker_scripts/
+RUN pip3 install --break-system-packages -r /docker_scripts/requirements.txt
+
+ARG user=jenkins
+RUN echo "${user}    ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
+USER "${user}"

docker/Dockerfile

@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC-BY-4.0
+
+services:
+  usage-plots:
+    image: ghcr.io/seqan/usage-plots
+    pull_policy: never
+    build:
+      context: .
+      additional_contexts:
+        config: ../scripts/config

docker/compose.yaml

@@ -1,4 +1,8 @@
 #!/usr/bin/env Rscript
 
-install.packages(c('ggplot2','scholar','knitr','rmarkdown','leaflet','rworldmap','lattice','RColorBrewer','sp'), repos='https://cloud.r-project.org/')
+initial.options <- commandArgs(trailingOnly = FALSE)
+script.dirname <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+libraries <- scan(file.path(script.dirname, "r-requirements.txt"), what="", sep="\n", quiet = TRUE)
+install.packages(libraries, repos='https://cloud.r-project.org/')
 q()

docker/docker_scripts/install_R_packages.R

@@ -10,13 +10,17 @@ apt-get install --yes --no-install-recommends \
     gawk \
     libabsl-dev \
     libcairo2-dev \
+    libfribidi-dev \
     libgdal-dev \
+    libharfbuzz-dev \
     libpng-dev \
     libssl-dev \
     libudunits2-dev \
+    nano \
     pandoc \
     python-is-python3 \
     python3 \
+    python3-pip \
     r-base \
     r-base-dev \
     sshpass \