Merge pull request #1 from khanlab/akhanf-patch-1

Update Dockerfile

.github/workflows/push_container.yml

@@ -5,7 +5,7 @@
 
 name: Publish Docker image
 
-on: 
+on:
   workflow_dispatch:
   release:
     types: [published]
@@ -18,22 +18,40 @@ jobs:
       packages: write
       contents: read
     steps:
+      - name: Maximize build space
+        uses: easimon/maximize-build-space@master
+        with:
+          remove-android: "true" # android-sdk
+          remove-codeql: "true" # code scanning
+          remove-dotnet: "true" # .net sdk
+          remove-haskell: "true" # haskell
+          remove-docker-images: "true" # rm existing cached images
+          overprovision-lvm: "true"
+
       - name: Check out the repo
         uses: actions/checkout@v2
-      
+
       - name: Log in to Docker Hub
         uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Extract metadata (tags, labels) for Docker
         id: meta
         uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
         with:
           images: |
             ${{ github.repository }}
-      
+            ghcr.io/${{ github.repository }}
+
       - name: Build and push Docker images
         uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
         with:

Dockerfile

@@ -1,8 +1,164 @@
-FROM mrtrix3/mrtrix3:3.0.3
+# Stage: python
+FROM nvidia/cuda:10.1-cudnn7-runtime-ubuntu18.04 as python
+ENV DEBIAN_FRONTEND="noninteractive" \
+    PYENV_VER="v2.3.17" \
+    PYTHON_VER="3.8.12" \
+    PYENV_ROOT="/opt/.pyenv" \
+    PATH="/opt/.pyenv/shims:/opt/.pyenv/bin:/usr/local/cuda/bin:${PATH}" \ 
+    LD_LIBRARY_PATH=/usr/local/cuda/lib64:${LD_LIBRARY_PATH}
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+    build-essential \
+    curl \
+    git \
+    libbz2-dev \
+    libffi-dev \ 
+    liblzma-dev \
+    libncurses5-dev \
+    libncursesw5-dev \
+    libreadline-dev \
+    libsqlite3-dev \ 
+    libssl-dev \
+    llvm \
+    python-openssl \
+    tk-dev \
+    wget \
+    xz-utils \
+    zlib1g-dev \
+    software-properties-common \
+    && git clone -b ${PYENV_VER} --depth=1 https://github.com/pyenv/pyenv.git /opt/.pyenv \
+    && pyenv install -v ${PYTHON_VER} \
+    && pyenv global ${PYTHON_VER} \
+    && python -m pip install --upgrade pip
 
-RUN apt-get -qq update \
-    && apt-get install -yq --no-install-recommends \
-        parallel \
-    && rm -rf /var/lib/apt/lists/*
+# Stage: builder
+# Notes: g++ (snakebids), tcsh (freesurfer), libtiff5 (mrtrix3)
+FROM python as builder
+RUN mkdir -p /opt \
+    && apt-get update -qq \ 
+    && apt-get install -y -q --no-install-recommends \
+    libeigen3-dev \
+    zlib1g-dev \
+    libqt5opengl5-dev \
+    libqt5svg5-dev \
+    libgl1-mesa-dev \
+    libncurses5 \
+    libxt6 \
+    libtiff5 \
+    parallel \
+    rsync \
+    tcsh \
+    g++ \
+    unzip \
+    bc \
+    # FSL dependencies
+    libexpat1-dev \
+    liblapack-dev \ 
+    libopenblas-dev \
+    libx11-dev \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+# Stage: ants
+FROM builder as ants
+ARG ANTS_VER=2.4.3
+RUN wget https://github.com/ANTsX/ANTs/releases/download/v${ANTS_VER}/ants-${ANTS_VER}-centos7-X64-gcc.zip -O ants.zip \
+    && unzip -qq ants.zip -d /opt \
+    && mv /opt/ants-${ANTS_VER} /opt/ants \
+    && rm ants.zip
 
+# Stage: fsl 
+FROM fnndsc/fsl:6.0.5.1-cuda9.1 as fsl
+RUN mv /usr/local/fsl/bin /usr/local/fsl/bin-all \
+    && mkdir -p /usr/local/fsl/bin \
+    && cd /usr/local/fsl/bin-all \
+    && cp -R bet* bedpost* topup applytopup eddy* fslorient probtrack* fslmerge remove_ext avscale /usr/local/fsl/bin \
+    && cd /usr/local/fsl/bin \
+    && rm -r eddy_cuda8.0 eddy_cuda10.2 /usr/local/fsl/bin-all 
+
+# Stage: itksnap (built with Ubuntu16.04 - glibc 2.23)
+FROM khanlab/itksnap:main as itksnap
+RUN cp -R /opt/itksnap/ /opt/itksnap-mini/ \
+    && cd /opt/itksnap-mini/bin \
+    && rm c2d itksnap* 
+
+# Stage: mrtrix (nogui)
+FROM builder as mrtrix
+ARG MRTRIX_VER=3.0.4
+ARG MRTRIX_CONFIG_FLAGS="-nogui"
+ARG MRTRIX_BUILD_FLAGS="" 
+RUN git clone --depth 1 https://github.com/MRtrix3/mrtrix3.git /opt/mrtrix3 \
+    && cd /opt/mrtrix3 \
+    && git fetch --tags \
+    && git checkout ${MRTRIX_VER} \
+    && ./configure ${MRTRIX_CONFIG_FLAGS} \
+    && ./build ${MRTRIX_BUILD_FLAGS} \
+    && mkdir -p mrtrix3_runtime \
+    && cp -R bin core lib src mrtrix3_runtime \ 
+    && rm -r tmp
+
+# Stage: niftyreg
+FROM builder as niftyreg
+ARG NIFTYREG_VER=1.3.9
+RUN wget https://sourceforge.net/projects/niftyreg/files/nifty_reg-${NIFTYREG_VER}/NiftyReg-${NIFTYREG_VER}-Linux-x86_64-Release.tar.gz/download -O /opt/niftyreg.tar.gz \
+    && tar -xf /opt/niftyreg.tar.gz -C /opt \
+    && mv /opt/NiftyReg-${NIFTYREG_VER}-Linux-x86_64-Release /opt/niftyreg \
+    && cd /opt/niftyreg/bin \ 
+    && ls . | grep -xv "reg_aladin" | xargs rm \
+    && rm /opt/niftyreg.tar.gz
+
+# Stage: synthstrip
+FROM freesurfer/synthstrip:1.3 as synthstrip
+
+# Stage: synthseg
+FROM builder as synthseg
+RUN git clone https://github.com/BBillot/Synthseg.git /opt/SynthSeg \
+    && curl https://www.dropbox.com/s/i62tzl821mqi3vd/synths_models_freesurfer_7.3.2.zip -Lo synthseg_models_freesurfer_7.3.2.zip \
+    && unzip -qqo synthseg_models_freesurfer_7.3.2.zip -d /opt/SynthSeg/models \
+    && rm synthseg_models_freesurfer_7.3.2.zip 
+
+# Stage: workbench
+FROM builder as workbench
+ARG WB_VER=1.5.0
+RUN wget https://humanconnectome.org/storage/app/media/workbench/workbench-linux64-v${WB_VER}.zip -O workbench.zip \
+    && unzip -qq workbench.zip -d /opt \
+    && rm -r /opt/workbench/plugins_linux64 \ 
+    && rm workbench.zip 
+
+# Stage: runtime
+FROM builder as runtime
+WORKDIR /
+COPY --from=ants \ 
+    # Commands to copy
+    /opt/ants/bin/antsApplyTransforms \
+    /opt/ants/bin/antsRegistration \ 
+    /opt/ants/bin/Atropos \ 
+    /opt/ants/bin/N4BiasFieldCorrection \ 
+    /opt/ants/bin/CreateJacobianDeterminantImage \
+    # Target destination
+    /opt/ants/bin/
+COPY --from=itksnap /opt/itksnap-mini /opt/itksnap/
+COPY --from=mrtrix /opt/mrtrix3/mrtrix3_runtime /opt/mrtrix3/
+COPY --from=niftyreg /opt/niftyreg /opt/niftyreg/
+COPY --from=synthseg /opt/SynthSeg /opt/SynthSeg/
+COPY --from=synthstrip /freesurfer /opt/freesurfer/
+COPY --from=workbench /opt/workbench /opt/workbench/
+# FSL + cuda9.1 
+COPY --from=fsl /usr/local/cuda /usr/local/cuda/
+COPY --from=fsl /usr/local/cuda-9.1 /usr/local/cuda-9.1/
+COPY --from=fsl /usr/local/fsl /usr/local/fsl/
+# Setup environments
+ENV OS=Linux \
+    ANTSPATH=/opt/ants/bin \
+    FREESURFER_HOME=/opt/freesurfer \ 
+    LD_LIBRARY_PATH=/opt/itksnap/lib:/opt/niftyreg/lib:/opt/workbench/libs_linux64:/opt/workbench/libs_linux64_software_opengl:${LD_LIBRARY_PATH}:/usr/local/cuda9.1/lib64:/usr/local/fsl/lib \
+    PATH=/opt/ants:/opt/ants/bin:/opt/freesurfer:/opt/itksnap/bin:/opt/mrtrix3/bin:/opt/niftyreg/bin/:/opt/workbench/bin_linux64:${PATH}:/usr/local/cuda9.1/bin:/usr/local/fsl/bin \
+    # FSL Options
+    FSLDIR=/usr/local/fsl \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    FSLMULTIFILEQUIT=TRUE \
+    FSLTCLSH=$FSLDIR/bin/fsltclsh \
+    FSLWISH=$FSLDIR/bin/fslwish
+COPY . /opt/pythondeps
+RUN pip install --prefer-binary --no-cache-dir /opt/pythondeps && apt-get purge -y -q curl g++ unzip wget \
+    && apt-get --purge -y -qq autoremove
+ENTRYPOINT ["/bin/bash"]

pyproject.toml

@@ -0,0 +1,28 @@
+[tool.poetry]
+name = "pythondeps"
+version = "0.1.0"
+description = "Containerized python environment"
+authors = ["Ali Khan <[email protected]>"]
+
+[tool.poetry.dependencies]
+python = ">=3.8,<3.12"
+matplotlib = "^3.5.2"
+nibabel = "^3.2.2"
+numpy = "^1.22.3"
+templateflow = "^0.8.1"
+PyPDF2 = "^1.27.12"
+nilearn = "^0.9.1"
+pandas = "^1.4.2"
+networkx = "^2.7.1"
+pillow = "9.0.1"
+pyvista = "^0.36.1"
+Pygments = "^2.11.2"
+snakebids = "^0.8.0"
+pybids = "0.15.6"
+
+
+[tool.poetry.dev-dependencies]
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"