Merge pull request #2578 from nipreps/fix/dockerfile-more-anaconda

ENH: Stop NeuroDebian dependency in Dockerfile

Dockerfile

@@ -25,33 +25,27 @@
 # Use Ubuntu 20.04 LTS
 FROM ubuntu:focal-20210416
 
-# Pre-cache neurodebian key
-COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
-ENV DEBIAN_FRONTEND="noninteractive" \
-    LANG="en_US.UTF-8" \
-    LC_ALL="en_US.UTF-8"
-
 # Prepare environment
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     apt-utils \
-                    curl \
+                    autoconf \
+                    build-essential \
                     bzip2 \
                     ca-certificates \
-                    xvfb \
-                    build-essential \
-                    autoconf \
+                    curl \
+                    git \
                     libtool \
+                    lsb-release \
                     pkg-config \
-                    graphviz \
-                    pandoc \
-                    pandoc-citeproc \
-                    git && \
-    curl -sSL https://deb.nodesource.com/setup_14.x | bash - && \
-    apt-get install -y --no-install-recommends \
-                    nodejs && \
+                    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 \
@@ -92,16 +86,6 @@ 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"
 
-# Installing Neurodebian packages
-RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /usr/local/etc/neurodebian.gpg && \
-    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-                    connectome-workbench=1.5.0-1~nd20.04+1 \
-                    git-annex-standalone=8.20210903-1~ndall+1 && \
-    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
 # FSL 5.0.11 (neurodocker build)
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
@@ -250,17 +234,14 @@ ENV PATH="/opt/afni-latest:$PATH" \
     AFNI_IMSAVE_WARNINGS="NO" \
     AFNI_PLUGINPATH="/opt/afni-latest"
 
-# Installing ANTs 2.3.4 (NeuroDocker build)
-ENV ANTSPATH="/usr/lib/ants" \
-    PATH="/usr/lib/ants:$PATH"
+# Installing ANTs 2.3.3 (NeuroDocker build)
+# Note: the URL says 2.3.4 but it is actually 2.3.3
+ENV ANTSPATH="/opt/ants" \
+    PATH="/opt/ants:$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
 
-# Installing SVGO and bids-validator
-RUN npm install -g svgo@^2.3 bids-validator@1.8.0 \
-  && rm -rf ~/.npm ~/.empty /root/.npm
-
 # Installing and setting up ICA_AROMA
 WORKDIR /opt/ICA-AROMA
 RUN curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
@@ -269,6 +250,17 @@ RUN curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
 ENV PATH="/opt/ICA-AROMA:$PATH" \
     AROMA_VERSION="0.4.5"
 
+WORKDIR /opt
+RUN curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
+    unzip workbench-linux64-v1.5.0.zip && \
+    rm workbench-linux64-v1.5.0.zip && \
+    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
+    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
+    # ABI tags can interfere when running on Singularity
+
+ENV PATH="/opt/workbench/bin_linux64:$PATH" \
+    LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
+
 # Installing and setting up miniconda
 RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh && \
     bash Miniconda3-py38_4.9.2-Linux-x86_64.sh -b -p /usr/local/miniconda && \
@@ -282,38 +274,50 @@ ENV PATH="/usr/local/miniconda/bin:$PATH" \
     PYTHONNOUSERSITE=1
 
 # Installing precomputed python packages
-RUN conda install -y python=3.8 \
-                     pip=21.0 \
-                     mkl=2021.2 \
-                     mkl-service=2.3 \
-                     numpy=1.20 \
-                     scipy=1.6 \
-                     scikit-learn=0.24 \
-                     scikit-image=0.18 \
+RUN conda install -y -c conda-forge -c anaconda \
+                     python=3.8 \
+                     git-annex=*=alldep* \
+                     graphviz=2.49 \
+                     libxml2=2.9 \
+                     libxslt=1.1 \
                      matplotlib=3.3 \
+                     mkl-service=2.4 \
+                     mkl=2021.3 \
+                     nodejs=16 \
+                     numpy=1.20 \
                      pandas=1.2 \
-                     libxslt=1.1 \
+                     pandoc=2.14 \
+                     pip=21.2 \
+                     scikit-image=0.18 \
+                     scikit-learn=0.24 \
+                     scipy=1.6 \
+                     setuptools=58.2 \
                      traits=6.2 \
-                     zstd=1.4; sync && \
+                     zlib=1.2 \
+                     zstd=1.5; sync && \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \
     conda clean -y --all && sync && \
     rm -rf ~/.conda ~/.cache/pip/*; sync
 
+# 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())" )
+
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
+# Installing SVGO and bids-validator
+RUN npm install -g svgo@^2.3 bids-validator@1.8.0 \
+  && rm -rf ~/.npm ~/.empty /root/.npm
+
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users fmriprep
 WORKDIR /home/fmriprep
 ENV HOME="/home/fmriprep"
 
-# 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())" )
-
 # Precaching atlases
 COPY scripts/fetch_templates.py fetch_templates.py
 
@@ -337,8 +341,6 @@ RUN find $HOME -type d -exec chmod go=u {} + && \
 
 ENV IS_DOCKER_8395080871=1
 
-# ABI tags can interfere when running on Singularity
-RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
 RUN ldconfig
 WORKDIR /tmp
 ENTRYPOINT ["/usr/local/miniconda/bin/fmriprep"]

fmriprep/cli/workflow.py

@@ -189,8 +189,7 @@ def build_boilerplate(config_file, workflow):
             "-s",
             "--bibliography",
             pkgrf("fmriprep", "data/boilerplate.bib"),
-            "--filter",
-            "pandoc-citeproc",
+            "--citeproc",
             "--metadata",
             'pagetitle="fMRIPrep citation boilerplate"',
             str(citation_files["md"]),