First commit

r-base-biosp and r-devel-biosp dockerfile CI/CD pipeline

First commit
r-base-biosp and r-devel-biosp dockerfile CI/CD pipeline
503a528b · Jean-Francois Rey · 503a528b · 503a528b · 503a528b · 503a528b
Commit 503a528b authored Oct 22, 2019 by Jean-Francois Rey ☕
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
+## Two stages
+# First to build docker images
+# Second to deploy in a server
+stages: 
+  - build_img
+  - deploy
+## Build docker image base on r-base
+## using DockerFile and register it in the 
+## docker registry of the project
+buildRBaseBioSP:
+  when: manual
+  tags:
+    - "dind"
+    - "docker"
+  variables:
+    DOCKER_TLS_CERTDIR: ""
+    DOCKER_HOST: tcp://docker:2375/
+    DOCKER_DRIVER: overlay2
+  services:
+    - docker:19.03.0-dind
+  before_script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  stage: build_img
+  script:
+    - docker build --no-cache --tag $CI_REGISTRY_IMAGE/r-base-biosp:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE/r-base-biosp:latest -f r-base-biosp/Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE/r-base-biosp:$CI_COMMIT_SHA
+    - docker push $CI_REGISTRY_IMAGE/r-base-biosp:latest
+  after_script:
+    - docker logout $CI_REGISTRY
+## Build docker image base on debian unstable and r-devel source
+## using DockerFile and register it in the 
+## docker registry of the project
+buildRDevelBioSP:
+  when: manual
+  tags:
+    - "dind"
+    - "docker"
+  variables:
+    DOCKER_TLS_CERTDIR: ""
+    DOCKER_HOST: tcp://docker:2375/
+    DOCKER_DRIVER: overlay2
+  services:
+    - docker:19.03.0-dind
+  before_script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  stage: build_img
+  script:
+    - docker build --no-cache --tag $CI_REGISTRY_IMAGE/r-devel-biosp:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE/r-devel-biosp:latest -f r-devel-biosp/Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE/r-devel-biosp:$CI_COMMIT_SHA
+    - docker push $CI_REGISTRY_IMAGE/r-devel-biosp:latest
+  after_script:
+    - docker logout $CI_REGISTRY
+## Deploy image on a server
+## Secret Variables:
+## DEPLOY_USER : user ID that have access to the server
+## DEPLOY_PWD : user password
+## DEPLOY_IP : server IP to deploy to
+deploy:
+  image: debian:stable
+  stage: deploy
+  when: manual
+  only:
+    - master
+  environment:
+    name: GitLabDockerRunners
+  before_script:
+    - apt-get update && apt-get install -y sshpass openssh-client
+    - export SSHPASS=$DEPLOY_PWD
+  script:
+    - sshpass -e ssh -o StrictHostKeyChecking=no $DEPLOY_USER@$DEPLOY_IP
+      "docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY;
+      docker pull $CI_REGISTRY_IMAGE/r-base-biosp:latest;
+      docker logout $CI_REGISTRY;"
+    - sshpass -e ssh -o StrictHostKeyChecking=no $DEPLOY_USER@$DEPLOY_IP
+      "docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY;
+      docker pull $CI_REGISTRY_IMAGE/r-devel-biosp:latest;
+      docker logout $CI_REGISTRY;"
--- a/LICENSE
+++ b/LICENSE
--- a/README.md
+++ b/README.md
+# Custom R Dockerfile
+R Docker image nigthly build :  
+* [R-base-biosp](r-base-biosp) : r-base + dependencies packages for R packaging pipeline
+* [R-devel-biosp](r-devel-biosp) : R devel version + dependencies packages for R packaging pipeline
+## CI/CD
+In your __.gitlab-ci.yml__ file use tags to select the docker image.
+```yaml
+tags:
+    - "r-base-biosp"
+```
+```yaml
+tags:
+    - "r-devel-biosp"
+```
+## Author 
+* Jean-François Rey <jean-francois.rey at inra.fr>
+## License
+[LICENSE](LICENSE)
--- a/r-base-biosp/Dockerfile
+++ b/r-base-biosp/Dockerfile
+FROM r-base:latest
+LABEL maintener="Jean-François Rey <jean-francois.rey@inra.fr>"
+LABEL description="r-base image for BioSP by adding packages dependencies"
+RUN echo "deb http://http.debian.net/debian sid main contrib non-free" > /etc/apt/sources.list.d/debian-unstable.list
+# install dependances
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+  sudo \
+  ntp \
+  libxml2 libxml2-dev \
+  gdal-bin libgdal-dev\
+  libfftw3-bin libfftw3-dev \
+  texlive texinfo \
+  texlive-fonts-extra \
+  libqpdf26 qpdf \
+  libudunits2-dev libudunits2-0 \
+  libgsl-dev \
+  libgeos-dev \
+  libgeos++-dev \
+  && apt-get clean \
+	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
+	&& rm -rf /var/lib/apt/lists/*
+# set France time zone
+ENV CONTAINER_TIMEZONE Europe/Paris
+ENV TZ Europe/Paris
+RUN sudo echo "Europe/Paris" > /etc/timezone
+RUN echo "fr_FR.UTF-8 UTF-8" >> /etc/locale.gen \
+  && locale-gen fr_FR.UTF8 \
+  && /usr/sbin/update-locale LANG=fr_FR.UTF-8
+ENV LC_ALL fr_FR.UTF-8
+ENV LANG fr_FR.UTF-8
+# install R packages
+#RUN Rscript -e "options(warn=2) ; install.packages(c('rgeos'), repos='https://cran.biotools.fr', dependencies=TRUE)"
+#with littler
+RUN install.r -r https://cran.biotools.fr -d TRUE -e \
+  deSolve \
+  methods \
+  grDevices \
+  graphics \
+  sp \
+  stats \
+  rgeos \
+  fields \
+  MASS \
+  Matrix \
+  rgeos \
+  deldir \
+  pracma \
+  raster \
+  fftwtools \
+  mvtnorm \
+  rgdal \
+  knitr \
+  maptools \
+  sf \
+  splancs \
+  RCALI \
+  rmarkdown \
+  testthat \
+  roxygen2 \
+  Rcpp \
+  RcppArmadillo \
+  fasterize \
+  shiny \
+  htmltools \
+  shinydashboard \
+  ggplot2 \
+  dplyr \
+  dbplyr \
+  DT \
+  magrittr \
+  devtools \
+  shinyjs \
+  stringi \
+  stringr \
+  jsonlite \
+  data.table \
+  htmlwidgets \
+  RSQLite \
+  BiocManager \
+  foreach \
+  doParallel \
+  mvtnorm \
+  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+RUN Rscript -e 'BiocManager::install(c("Biostrings"))'
+# force update to last version
+RUN Rscript -e "update.packages(ask=FALSE)"
+#ENTRYPOINT ["/bin/sh", "-c"]
+WORKDIR /home/docker
+CMD ["R"]
--- a/r-base-biosp/README.md
+++ b/r-base-biosp/README.md
+# Custom R-base image
+This is a custom R-base image use as runner for CI/CD pipeline.
--- a/r-devel-biosp/Dockerfile
+++ b/r-devel-biosp/Dockerfile
+FROM debian:unstable
+LABEL maintener="Jean-François Rey <jean-francois.rey@inra.fr>"
+LABEL description="r-devel image for BioSP by adding packages dependencies"
+RUN useradd docker \
+	&& mkdir /home/docker \
+	&& chown docker:docker /home/docker \
+	&& addgroup docker staff
+RUN echo 'deb http://deb.debian.org/debian testing main' >> /etc/apt/source.list && apt-get update -qq \
+	&& apt-get install -t unstable -y --no-install-recommends \
+    ed \
+		less \
+		locales \
+		vim-tiny \
+		wget \
+		ca-certificates \
+		fonts-texgyre \
+		ntp \
+		tzdata \
+		rsync \
+		bash-completion \
+		bison \
+		debhelper \
+		default-jdk \
+		g++ \
+		gcc \
+		gdb \
+		gfortran \
+		groff-base \
+		libblas-dev \
+		libbz2-dev \
+		libcairo2-dev/unstable \
+		libcurl4-openssl-dev \
+    gdal-bin \
+    libgdal-dev \
+    libgeos-dev \
+    libgeos++-dev \
+		libjpeg-dev \
+		liblapack-dev \
+		liblzma-dev \
+    #libnetcdf-dev \
+		libncurses5-dev \
+		libpango1.0-dev \
+		libpcre3-dev \
+		libpng-dev \
+		libreadline-dev \
+		libtiff5-dev \
+		libx11-dev \
+		libxt-dev \
+    libxml2 \
+    libxml2-dev \
+    #libgdal-dev \
+    #libgdal20 \
+    #libhdf5-100 \
+    #libnetcdf13 libnetcdf-dev \
+    #libarmadillo-dev libhdf5-dev libnetcdf-dev \
+    libfftw3-bin libfftw3-dev \
+    #libhdf5-103 libhdf5-cpp-103 \
+    mesa-common-dev \
+    libglu1-mesa-dev \
+		mpack \
+    openssl \
+    libssl-dev \
+		subversion \
+		tcl8.6-dev \
+		texinfo \
+		texlive-base \
+		texlive-extra-utils \
+		texlive-fonts-extra \
+		texlive-fonts-recommended \
+		texlive-generic-recommended \
+		texlive-latex-base \
+		texlive-latex-extra \
+		texlive-latex-recommended \
+		tk8.6-dev \
+		x11proto-core-dev \
+		xauth \
+		xdg-utils \
+		xfonts-base \
+		xvfb \
+		zlib1g-dev \
+    qpdf \
+    libudunits2-dev libudunits2-0 \
+    libgsl-dev \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/*
+## Set timezone
+ENV CONTAINER_TIMEZONE Europe/Paris
+ENV TZ Europe/Paris
+RUN echo "Europe/Paris" > /etc/timezone
+RUN echo "fr_FR.UTF-8 UTF-8" >> /etc/locale.gen \
+  && locale-gen fr_FR.UTF8 \
+  && /usr/sbin/update-locale LANG=fr_FR.UTF-8
+ENV LC_ALL fr_FR.UTF-8
+ENV LANG fr_FR.UTF-8
+## Checkout R-Devel
+RUN cd /home/docker/ \
+&& svn co https://svn.r-project.org/R/trunk R-devel
+#Build R-devel
+RUN cd /home/docker/R-devel \
+&& ./tools/rsync-recommended \
+&& ./configure --enable-memory-profiling \
+		--enable-R-profiling \
+		--with-valgrind-instrumentation \
+		--with-system-valgrind-headers \
+		CFLAGS=" -Wall -Wextra -g -ggdb -Wconversion -O0" \
+		CXXFLAGS=" -Wall -Wextra -g -ggdb -Wconversion -O0 -fno-inline" \
+&& make -j 4 \ 
+&& make install \
+&& cd /home/docker/ \
+&& rm -rf R-devel/
+#RUN cd /home/docker/R-devel &&  make install-tests \
+#  && cd tests \
+#  && ../bin/R CMD make check \
+#  && ../bin/R CMD make check-devel \
+#  && ../bin/R CMD make check-all
+# R config
+RUN echo 'options(repos=c(CRAN="https://cran.biotools.fr"), \
+  download.file.method = "libcurl")' >> /usr/local/lib/R/etc/Rprofile.site
+#RUN echo "options(warn=2) ; install.packages(c( \
+RUN echo "install.packages(c( \
+  'deSolve', \
+  'sp', \
+  'rgeos', \
+  'fields', \
+  'MASS', \
+  'Matrix', \
+  'deldir', \
+  'pracma', \
+  'raster', \
+  'fftwtools', \
+  'mvtnorm', \
+  'rgdal', \
+  'sf', \
+  'splancs', \
+  'knitr', \
+  'rmarkdown', \
+  'testthat', \
+  'Rcpp', \
+  'RcppArmadillo', \
+  'fasterize', \
+  'roxygen2', \
+  'shiny', \
+  'htmltools', \
+  'shinydashboard', \
+  'ggplot2', \
+  'dplyr', \
+  'dbplyr', \
+  'DT', \
+  'magrittr', \
+  'devtools', \
+  'shinyjs', \
+  'stringi', \
+  'stringr', \
+  'jsonlite', \
+  'data.table', \
+  'htmlwidgets', \
+  'RSQLite', \
+  'BiocManager', \
+  'foreach', \
+  'doParallel' \
+  'mvtnorm' \
+  ), \
+  dependencies=TRUE, \
+  repos='https://cran.biotools.fr')" > /tmp/install.R \
+  && Rscript /tmp/install.R
+RUN Rscript -e 'BiocManager::install(c("Biostrings"))'
+RUN Rscript -e "update.packages(ask=FALSE)"
+WORKDIR /home/docker
+USER docker
+CMD ["R"]
--- a/r-devel-biosp/README.md
+++ b/r-devel-biosp/README.md
+# Custom R-devel image
+This is a custom R-devel image use as runner for CI/CD pipeline.  
+It bases on debian:unstable and last r-devel version.