chore: Merge branch 'main' of https://github.com/CCBR/reneeTools

.Rbuildignore

@@ -10,3 +10,4 @@
 ^\.prettierignore$
 ^\.prettierrc$
 ^data-raw$
+^Dockerfile$

.github/workflows/docker.yml

@@ -0,0 +1,57 @@
+name: docker
+
+on:
+  # push:
+  #   paths:
+  #     - ".github/workflows/docker.yml"
+  #     - "DESCRIPTION"
+  #     - "Dockerfile"
+  workflow_dispatch:
+  release:
+    types: [published]
+
+env:
+  IMAGE_NAME: "reneetools"
+  CONTEXT: "./"
+  NAMESPACE: "nciccbr"
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Prepare build-time variables
+        id: vars
+        run: |
+          echo "DATE=$(date +"%Y-%m-%d")" >> "$GITHUB_OUTPUT"
+
+          if [ '${{ github.event_name }}' == 'release' ]; then
+            VERSION=${{ github.ref_name }}
+          else
+            HASH=$(echo "${{ github.sha }}" | cut -c1-7)
+            VERSION="$(grep 'Version:' $CONTEXT/DESCRIPTION | sed 's/Version: //')_$HASH"
+          fi
+          echo "VERSION_TAG=$(echo $VERSION)" >> "$GITHUB_OUTPUT"
+      - name: debug
+        run: |
+          echo "the github tag is ${{ github.ref_name }}"
+          echo "github event_name is ${{ github.event_name }}"
+          echo "the version tag is ${{ steps.vars.outputs.VERSION_TAG }}"
+
+      - name: Login to DockerHub
+        if: ${{ github.event_name != 'pull_request' }}
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ env.NAMESPACE }}/${{ env.IMAGE_NAME }}:${{ steps.vars.outputs.VERSION_TAG }}
+          context: ${{ env.CONTEXT }}
+          file: ${{ env.CONTEXT }}/Dockerfile
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.DATE }}
+            BUILD_TAG=${{ steps.vars.outputs.VERSION_TAG }}
+            REPONAME=${{ env.IMAGE_NAME }}

DESCRIPTION

@@ -23,6 +23,7 @@ Imports:
 Suggests:
     readr,
     testthat (>= 3.0.0)
+biocViews:
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true

Dockerfile

@@ -0,0 +1,96 @@
+FROM ubuntu:20.04
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+RUN mkdir -p /opt2 && mkdir -p /data2
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+RUN apt update && apt-get -y upgrade
+# Set the locale
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+		locales build-essential cmake cpanminus && \
+	localedef -i en_US -f UTF-8 en_US.UTF-8 && \
+	cpanm FindBin Term::ReadLine
+
+# install basic dependencies with apt-get
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+  build-essential \
+	g++ \
+	gcc \
+	gfortran \
+	git \
+	libatlas-base-dev \
+	libblas-dev \
+	libboost-dev \
+	libbz2-dev \
+	libcurl4-openssl-dev \
+	libexpat1-dev \
+	libfreetype6-dev \
+	libgd-dev \
+	libgd-perl \
+	libglib2.0-dev \
+  libgpgme11-dev \
+	libgs-dev \
+	libgsl-dev \
+	libgsl0-dev \
+	libhtml-template-compiled-perl \
+	libicu-dev \
+	libjudy-dev \
+	liblapack-dev \
+	liblzma-dev \
+	libmysqlclient-dev \
+	libncurses-dev \
+	libopenmpi-dev \
+	libpng-dev \
+	librtmp-dev \
+  libseccomp-dev \
+	libssl-dev \
+	libtool \
+	libxml-libxml-debugging-perl \
+	libxml-opml-simplegen-perl \
+	libxml2-dev \
+	libxslt-dev \
+	make \
+	manpages-dev \
+	openjdk-17-jre-headless \
+	parallel \
+	pigz \
+  pkg-config \
+	rsync \
+  squashfs-tools \
+	unzip \
+  uuid-dev \
+	wget \
+	zlib1g \
+	zlib1g-dev \
+	zlibc
+
+# Install conda and give write permissions to conda folder
+RUN echo 'export PATH=/opt2/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+    wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O ~/miniforge3.sh && \
+    /bin/bash ~/miniforge3.sh -b -p /opt2/conda && \
+    rm ~/miniforge3.sh && chmod 777 -R /opt2/conda/
+ENV PATH="/opt2/conda/bin:$PATH"
+
+# install devtools
+RUN mamba install -c conda-forge r-base=4.3.2 r-devtools
+
+# install R package
+COPY . /opt2/reneeTools
+RUN R -e 'devtools::install("/opt2/reneeTools")'
+
+# cleanup
+RUN apt-get clean && apt-get purge && \
+  rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+COPY Dockerfile /opt2/Dockerfile
+RUN chmod -R a+rX /opt2/Dockerfile
+
+WORKDIR /data2