MAINT: Use the base nipreps/miniconda image

.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

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="" \
@@ -79,122 +86,214 @@ 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 {} + && \
+RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
+    mkdir -p $HOME/.cache/dmriprep && \
+    mkdir -p $HOME/.nipype && \
+    find $HOME -type d -exec chmod go=u {} + && \
     find $HOME -type f -exec chmod go=u {} +
 
+# Refresh linked libraries
+RUN ldconfig
+
 WORKDIR /tmp/
-ENTRYPOINT ["/usr/local/miniconda/bin/dmriprep"]
+ENTRYPOINT ["/opt/conda/bin/dmriprep"]
 
 ARG BUILD_DATE
 ARG VCS_REF