Major update: Add gpu support to Bioconductor containers [WIP]

.github/workflows/weekly-build-bioc-ml.yaml

@@ -0,0 +1,60 @@
+name: Bioc ML-GPU image weekly build
+
+on:
+  push:
+    branches:
+      - 'add_gpu_support'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout rocker/versioned2 repo
+        uses: actions/checkout@v3
+        with:
+          repository: rocker-org/rocker-versioned2
+          path: rocker-versioned2
+
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Build and export
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: dockerfiles/r-ver_devel.Dockerfile
+          tags: rocker/r-ver:devel
+          outputs: type=docker,dest=/tmp/rverdevel.tar
+      -
+        name: Upload artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: r-ver
+          path: /tmp/rverdevel.tar
+
+      # -
+      #   name: Checkout
+      #   uses: actions/checkout@v2
+
+  use:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Download artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: myimage
+          path: /tmp
+      -
+        name: Load image
+        run: |
+          docker load --input /tmp/myimage.tar
+          docker image ls -a
+
+

.scripts/weekly_build_ml.sh

@@ -0,0 +1,63 @@
+set -e
+echo "Build bioconductor_docker image"
+
+###############################################
+## Step 0: Set up variables and clone
+## Rocker repo
+ROCKER_REPO=https://github.com/rocker-org/rocker-versioned2
+
+## git clone rocker
+git clone --depth 1 $ROCKER_REPO
+
+###############################################
+## 1. docker build rocker r-ver: repo
+
+cd rocker-versioned2/
+
+#################################################################
+## NOTE: This needs to change when it comes time for RELEASE_3_12
+##
+## The R_VERSION in the dockerfile for r-ver needs to be changed to
+## 'ENV R_VERSION=patched' during this release cycle.
+##
+## This will be done with the help of "sed"
+
+#sed -r -i 's/ENV R_VERSION=4.0.2/ENV R_VERSION=patched/g' dockerfiles/r-ver_4.0.2.Dockerfile
+
+#################################################################
+
+docker build -t rocker/r-ver:devel -f dockerfiles/r-ver_devel.Dockerfile .
+
+###############################################
+## 2. docker build rocker/cuda:devel
+
+echo "*** Building rocker/cuda:devel *** \n"
+
+docker build -t rocker/cuda:devel -f dockerfiles/cuda_devel.Dockerfile .
+
+###############################################
+## 3. docker build nitesh1989/bioconductor_ml:devel
+
+cd $GITHUB_WORKSPACE;
+
+echo "*** Building nitesh1989/bioconductor_ml *** \n"
+
+## increment version number with sed
+sed -r -i 's/(^ARG BIOCONDUCTOR_PATCH=)([0-9]+)$/echo "\1$((\2+1))"/ge' Dockerfile
+
+## Git login
+git config user.email "[email protected]"
+git config user.name "bioc-docker-bot"
+
+## Git commit
+git commit -am "Weekly version bump and rebuild of nitesh1989/bioconductor_ml:devel"
+
+## docker build, login and push
+docker build -t nitesh1989/bioconductor_ml:devel -f dockerfiles/bioc_ml_devel.Dockerfile .
+
+docker login --username=$DOCKER_USERNAME --password=$DOCKER_PASSWORD
+
+docker push nitesh1989/bioconductor_ml:devel
+
+## Finish
+echo "Done"

bioc_scripts/add_bioc_devel_env_variables.sh

@@ -0,0 +1,9 @@
+# Variables in Renviron.site are made available inside of R.
+# Add libsbml CFLAGS
+
+curl -O http://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc \
+    && cat Renviron.bioc | grep -o '^[^#]*' | sed 's/export //g' >>/etc/environment \
+    && cat Renviron.bioc >> /usr/local/lib/R/etc/Renviron.site \
+    && echo 'LIBSBML_CFLAGS="-I/usr/include"' >> /usr/local/lib/R/etc/Renviron.site \
+    && echo 'LIBSBML_LIBS="-lsbml"' >> /usr/local/lib/R/etc/Renviron.site \
+    && rm -rf Renviron.bioc

bioc_scripts/conda-tensorflow-env.yaml

@@ -0,0 +1,13 @@
+name: conda-tensorflow-env
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.9
+  - anaconda
+  - pip
+  - git
+  ## Scientific Computing
+  - numpy
+  - scipy
+  - tensorflow-gpu

bioc_scripts/install-conda.sh

@@ -0,0 +1,19 @@
+wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh \
+    && /bin/bash ~/miniconda.sh -b -p /opt/conda \
+    && rm -f ~/miniconda.sh
+
+## https://docs.anaconda.com/anaconda/install/multi-user/ -
+## Multi user conda installation -
+## Install conda for both rstudio user and root -
+## make sure the "env" is available to both users
+groupadd condausers
+chgrp -R condausers /opt/conda
+chmod 770 -R /opt/conda
+
+## Add rstudio to condausers group
+adduser rstudio condausers
+
+## Make sure conda works on "rstudio" user as well
+cat <<"EOF">>/etc/bash.bashrc
+PATH=/opt/conda/bin:$PATH
+EOF

dockerfiles/bioconductor_ml.Dockerfile

@@ -0,0 +1,51 @@
+# The suggested name for this image is: bioconductor/bioconductor_docker:devel
+FROM rocker/ml:4.2.0
+
+## Set Dockerfile version number
+ARG BIOCONDUCTOR_VERSION=3.16
+
+##### IMPORTANT ########
+## The PATCH version number should be incremented each time
+## there is a change in the Dockerfile.
+ARG BIOCONDUCTOR_PATCH=0
+ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
+
+LABEL name="bioconductor/bioconductor_docker" \
+      version=$BIOCONDUCTOR_DOCKER_VERSION \
+      url="https://github.com/Bioconductor/bioconductor_docker" \
+      vendor="Bioconductor Project" \
+      maintainer="[email protected]" \
+      description="Bioconductor docker image with system dependencies to install all packages." \
+      license="Artistic-2.0"
+
+##  Add Bioconductor Requirements
+ADD bioc_scripts /tmp/bioc_scripts
+
+## Add host-site-library
+## Set PIP_USER=false
+RUN echo "R_LIBS=/usr/local/lib/R/host-site-library:\${R_LIBS}" > /usr/local/lib/R/etc/Renviron.site \
+    && echo "BIOCONDUCTOR_VERSION=${BIOCONDUCTOR_VERSION}" >> /usr/local/lib/R/etc/Renviron.site \
+    && echo "BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_DOCKER_VERSION}" >> /usr/local/lib/R/etc/Renviron.site \
+    && echo "PIP_USER=false" >> /usr/local/lib/R/etc/Renviron.site
+
+# 1. Install Bioconductor system depdencies
+RUN bash /tmp/bioc_scripts/install_bioc_sysdeps.sh
+
+# 2. Install specific version of BiocManager and libraries
+RUN R -f /tmp/bioc_scripts/install.R
+
+# 3. DEVEL: Add sys env variables to DEVEL image
+RUN bash /tmp/bioc_scripts/add_bioc_devel_env_variables.sh
+
+# 4. Install conda
+RUN bash /tmp/bioc_scripts/install-conda.sh
+ENV PATH="/opt/conda/bin:${PATH}"
+
+# Add Env variables for specific packages
+ENV LIBSBML_CFLAGS="-I/usr/include"
+ENV LIBSBML_LIBS="-lsbml"
+ENV BIOCONDUCTOR_DOCKER_VERSION=$BIOCONDUCTOR_DOCKER_VERSION
+ENV BIOCONDUCTOR_VERSION=$BIOCONDUCTOR_VERSION
+
+# Init command for s6-overlay
+CMD ["/init"]