MAINT: Use the base nipreps/miniconda image

This should ease the issues we are having with some dependencies (esp. hdf5) as well as make the building process more standardized across nipreps. In the long run it should also help minimize build time, as we converge towards multi-stage builds where source images have been minimized.
nipreps · Oct 25, 2021 · 300bb16 · 300bb16
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commit 300bb16
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -74,14 +74,14 @@ jobs:
             set -e
             if [[ "$success" = "0" ]]; then
                 echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:xenial-20201030
+                docker tag localhost:5000/ubuntu ubuntu:focal-20210416
                 docker pull localhost:5000/dmriprep
                 docker tag localhost:5000/dmriprep nipreps/dmriprep:latest
                 docker tag localhost:5000/dmriprep nipreps/dmriprep
             else
                 echo "Pulling from Docker Hub"
-                docker pull ubuntu:xenial-20201030
-                docker tag ubuntu:xenial-20201030 localhost:5000/ubuntu
+                docker pull ubuntu:focal-20210416
+                docker tag ubuntu:focal-20210416 localhost:5000/ubuntu
                 docker push localhost:5000/ubuntu
                 docker pull nipreps/dmriprep:latest
             fi

diff --git a/Dockerfile b/Dockerfile
@@ -22,27 +22,33 @@
 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 # SOFTWARE.
 
-# Use Ubuntu 16.04 LTS
-FROM ubuntu:xenial-20201030
+# Use Ubuntu 20.04 LTS
+FROM ubuntu:focal-20210416
 
 # Prepare environment
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
+                    apt-utils \
                     autoconf \
                     build-essential \
                     bzip2 \
                     ca-certificates \
                     curl \
-                    cython3 \
                     git \
                     libtool \
                     lsb-release \
                     pkg-config \
+                    unzip \
                     xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+ENV DEBIAN_FRONTEND="noninteractive" \
+    LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8"
+
 # Installing freesurfer
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \
+    | tar zxv --no-same-owner -C /opt \
     --exclude='freesurfer/diffusion' \
     --exclude='freesurfer/docs' \
     --exclude='freesurfer/fsfast' \
@@ -62,7 +68,8 @@ RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/frees
     --exclude='freesurfer/subjects/V1_average' \
     --exclude='freesurfer/trctrain'
 
-ENV FSL_DIR="/usr/share/fsl/5.0" \
+# Simulate SetUpFreeSurfer.sh
+ENV FSL_DIR="/opt/fsl-5.0.11" \
     OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
@@ -79,119 +86,209 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
-# Pre-cache neurodebian key
-COPY .docker/neurodebian.gpg /usr/local/etc/neurodebian.gpg
-# Installing Neurodebian packages (FSL, AFNI, git)
-RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /usr/local/etc/neurodebian.gpg && \
-    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-                    fsl-core=5.0.9-5~nd16.04+1 \
-                    fsl-mni152-templates=5.0.7-2 \
-                    afni=16.2.07~dfsg.1-5~nd16.04+1 \
-                    convert3d && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-ENV FSLDIR="/usr/share/fsl/5.0" \
+# FSL 5.0.11 (neurodocker build)
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libgl1-mesa-dri \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           sudo \
+           wget \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /opt/fsl-5.0.11 \
+    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
+    --exclude "fsl/config" \
+    --exclude "fsl/data/atlases" \
+    --exclude "fsl/data/first" \
+    --exclude "fsl/data/mist" \
+    --exclude "fsl/data/possum" \
+    --exclude "fsl/data/standard/bianca" \
+    --exclude "fsl/data/standard/tissuepriors" \
+    --exclude "fsl/doc" \
+    --exclude "fsl/etc/default_flobs.flobs" \
+    --exclude "fsl/etc/fslconf" \
+    --exclude "fsl/etc/js" \
+    --exclude "fsl/etc/luts" \
+    --exclude "fsl/etc/matlab" \
+    --exclude "fsl/extras" \
+    --exclude "fsl/include" \
+    --exclude "fsl/python" \
+    --exclude "fsl/refdoc" \
+    --exclude "fsl/src" \
+    --exclude "fsl/tcl" \
+    --exclude "fsl/bin/FSLeyes" \
+    && find /opt/fsl-5.0.11/bin -type f -not \( \
+        -name "applywarp" -or \
+        -name "bet" -or \
+        -name "bet2" -or \
+        -name "convert_xfm" -or \
+        -name "fast" -or \
+        -name "flirt" -or \
+        -name "fsl_regfilt" -or \
+        -name "fslhd" -or \
+        -name "fslinfo" -or \
+        -name "fslmaths" -or \
+        -name "fslmerge" -or \
+        -name "fslroi" -or \
+        -name "fslsplit" -or \
+        -name "fslstats" -or \
+        -name "imtest" -or \
+        -name "mcflirt" -or \
+        -name "melodic" -or \
+        -name "prelude" -or \
+        -name "remove_ext" -or \
+        -name "susan" -or \
+        -name "topup" -or \
+        -name "zeropad" \) -delete \
+    && find /opt/fsl-5.0.11/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
+ENV FSLDIR="/opt/fsl-5.0.11" \
+    PATH="/opt/fsl-5.0.11/bin:$PATH" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
     FSLMULTIFILEQUIT="TRUE" \
-    POSSUMDIR="/usr/share/fsl/5.0" \
-    LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
-    FSLTCLSH="/usr/bin/tclsh" \
-    FSLWISH="/usr/bin/wish" \
-    AFNI_MODELPATH="/usr/lib/afni/models" \
-    AFNI_IMSAVE_WARNINGS="NO" \
-    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
-    AFNI_PLUGINPATH="/usr/lib/afni/plugins"
-ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q" \
+    LD_LIBRARY_PATH="/opt/fsl-5.0.11/lib:$LD_LIBRARY_PATH"
 
-COPY .docker/fsl-6.0/bin/topup /usr/share/fsl/5.0/bin/topup
-COPY .docker/fsl-6.0/bin/imglob /usr/share/fsl/5.0/bin/imglob
-COPY .docker/fsl-6.0/bin/eddy_openmp  /usr/lib/fsl/5.0/eddy_openmp
-COPY .docker/fsl-6.0/lib/* /usr/lib/fsl/5.0/
+# Override some FSL tools with the version 6.0 binaries
+COPY .docker/fsl-6.0/bin/topup /opt/fsl-5.0.11/bin/topup
+COPY .docker/fsl-6.0/bin/imglob /opt/fsl-5.0.11/bin/imglob
+COPY .docker/fsl-6.0/bin/eddy_openmp /opt/fsl-5.0.11/eddy_openmp
+COPY .docker/fsl-6.0/lib/* /opt/fsl-5.0.11/lib/
+
+# Convert3D (neurodocker build)
+RUN echo "Downloading Convert3D ..." \
+    && mkdir -p /opt/convert3d-1.0.0 \
+    && curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
+    | tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
+    --exclude "c3d-1.0.0-Linux-x86_64/lib" \
+    --exclude "c3d-1.0.0-Linux-x86_64/share" \
+    --exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
+ENV C3DPATH="/opt/convert3d-1.0.0" \
+    PATH="/opt/convert3d-1.0.0/bin:$PATH"
+
+# AFNI latest (neurodocker build)
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           ed \
+           gsl-bin \
+           libglib2.0-0 \
+           libglu1-mesa-dev \
+           libglw1-mesa \
+           libgomp1 \
+           libjpeg62 \
+           libxm4 \
+           netpbm \
+           tcsh \
+           xfonts-base \
+           xvfb \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.2_amd64.deb \
+    && dpkg -i /tmp/multiarch.deb \
+    && rm /tmp/multiarch.deb \
+    && curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
+    && dpkg -i /tmp/libxp6.deb \
+    && rm /tmp/libxp6.deb \
+    && curl -sSL --retry 5 -o /tmp/libpng.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
+    && dpkg -i /tmp/libpng.deb \
+    && rm /tmp/libpng.deb \
+    && apt-get install -f \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
+    && if [ -n "$gsl2_path" ]; then \
+         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
+    fi \
+    && ldconfig \
+    && echo "Downloading AFNI ..." \
+    && mkdir -p /opt/afni-latest \
+    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
+    | tar -xz -C /opt/afni-latest --strip-components 1 \
+    --exclude "linux_openmp_64/*.gz" \
+    --exclude "linux_openmp_64/funstuff" \
+    --exclude "linux_openmp_64/shiny" \
+    --exclude "linux_openmp_64/afnipy" \
+    --exclude "linux_openmp_64/lib/RetroTS" \
+    --exclude "linux_openmp_64/meica.libs" \
+    # Keep only what we use
+    && find /opt/afni-latest -type f -not \( \
+        -name "3dTshift" -or \
+        -name "3dUnifize" -or \
+        -name "3dAutomask" -or \
+        -name "3dvolreg" \) -delete
+
+ENV PATH="/opt/afni-latest:$PATH" \
+    AFNI_IMSAVE_WARNINGS="NO" \
+    AFNI_PLUGINPATH="/opt/afni-latest"
 
 # Installing ANTs 2.3.3 (NeuroDocker build)
 # Note: the URL says 2.3.4 but it is actually 2.3.3
-ENV ANTSPATH=/usr/lib/ants
-RUN mkdir -p $ANTSPATH && \
-    curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
+ENV ANTSPATH="/opt/ants" \
+    PATH="/opt/ants:$PATH"
+WORKDIR $ANTSPATH
+RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
     | tar -xzC $ANTSPATH --strip-components 1
-ENV PATH=$ANTSPATH:$PATH
 
-# Create a shared $HOME directory
-RUN useradd -m -s /bin/bash -G users dmriprep
-WORKDIR /home/dmriprep
-ENV HOME="/home/dmriprep"
+COPY --from=nipreps/miniconda@sha256:4d0dc0fabb794e9fe22ee468ae5f86c2c8c2b4cd9d7b7fdf0c134d9e13838729 /opt/conda /opt/conda
 
-# Installing and setting up miniconda
-RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \
-    bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \
-    rm Miniconda3-4.5.11-Linux-x86_64.sh
+RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
 
 # Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
-ENV PATH="/usr/local/miniconda/bin:$PATH" \
-    CPATH="/usr/local/miniconda/include/:$CPATH" \
+ENV PATH="/opt/conda/bin:$PATH" \
+    CPATH="/opt/conda/include:$CPATH" \
+    LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
     LANG="C.UTF-8" \
     LC_ALL="C.UTF-8" \
     PYTHONNOUSERSITE=1
 
-# Installing precomputed python packages
-RUN conda install -y -c anaconda -c conda-forge \
-                     python=3.7.1 \
-                     graphviz=2.40 \
-                     git-annex \
-                     libxml2=2.9.8 \
-                     libxslt=1.1.32 \
-                     matplotlib=2.2 \
-                     mkl \
-                     mkl-service \
-                     nodejs \
-                     numpy=1.20 \
-                     pandoc=2.11 \
-                     pip=20.3 \
-                     scikit-learn=0.19 \
-                     scipy=1.5 \
-                     setuptools=51.1 \
-                     traits=4.6.0 \
-                     zlib; sync && \
-    chmod -R a+rX /usr/local/miniconda; sync && \
-    chmod +x /usr/local/miniconda/bin/*; sync && \
-    conda build purge-all; sync && \
-    conda clean -tipsy && sync
-
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
-# Precaching fonts, set 'Agg' as default backend for matplotlib
-RUN python -c "from matplotlib import font_manager" && \
-    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
-
-# Installing SVGO
-RUN npm install -g svgo
-
-# Installing bids-validator
-RUN npm install -g [email protected]
-
-# Refresh linked libraries
-RUN ldconfig
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users dmriprep
+WORKDIR /home/dmriprep
+ENV HOME="/home/dmriprep"
 
-WORKDIR /src
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
+    echo "conda activate base" >> $HOME/.bashrc
 
 # Installing dMRIPrep
 COPY . /src/dmriprep
 ARG VERSION
 # Force static versioning within container
 RUN echo "${VERSION}" > /src/dmriprep/dmriprep/VERSION && \
     echo "include dmriprep/VERSION" >> /src/dmriprep/MANIFEST.in && \
-    cd /src/dmriprep && \
-    pip install --no-cache-dir .[all]
+    /opt/conda/bin/python -m pip install --no-cache-dir "/src/dmriprep[all]"
 
 RUN find $HOME -type d -exec chmod go=u {} + && \
-    find $HOME -type f -exec chmod go=u {} +
+    find $HOME -type f -exec chmod go=u {} + && \
+    rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
+
+# Refresh linked libraries
+RUN ldconfig
 
 WORKDIR /tmp/
 ENTRYPOINT ["/usr/local/miniconda/bin/dmriprep"]