Reorganize installation steps (#5)

* Reorder things a bit. * Update Dockerfile * Move conda install to above afni install.
PennLINC · Feb 13, 2023 · f5a9204 · f5a9204
1 parent 8961b18
commit f5a9204
Showing 1 changed file with 68 additions and 67 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,30 +1,30 @@
-
 FROM ubuntu:bionic-20220531
 
 COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
 
 # Prepare environment
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    apt-utils \
-                    wget \
-                    curl \
-                    bzip2 \
-                    locales \
-                    unzip \
-                    ca-certificates \
-                    xvfb \
-                    build-essential \
-                    autoconf \
-                    libtool \
-                    pkg-config \
-                    graphviz \
-                    pandoc \
-                    pandoc-citeproc \
-                    git && \
+        apt-utils \
+        autoconf \
+        build-essential \
+        bzip2 \
+        ca-certificates \
+        curl \
+        git \
+        graphviz \
+        libtool \
+        locales \
+        pandoc \
+        pandoc-citeproc \
+        pkg-config \
+        unzip \
+        wget \
+        xvfb \
+        && \
     curl -sSL https://deb.nodesource.com/setup_14.x | bash - && \
     apt-get install -y --no-install-recommends \
-                    nodejs && \
+        nodejs && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ENV OS="Linux" \
@@ -41,14 +41,49 @@ RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca
     apt-key add /usr/local/etc/neurodebian.gpg && \
     (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
 
+
+# Install 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 && \
+    rm Miniconda3-py38_4.9.2-Linux-x86_64.sh
+
+# 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" \
+    LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1
+
+# Install precomputed python packages
+RUN conda install -y \
+        python=3.8 \
+        libxslt=1.1 \
+        matplotlib=3.3 \
+        mkl=2021.2 \
+        mkl-service=2.3 \
+        numpy=1.18.1 \
+        pandas=1.2 \
+        pip=21.0 \
+        scikit-learn=0.24 \
+        scipy=1.6 \
+        traits=6.2 \
+        zstd=1.4; \
+    sync && \
+    chmod -R a+rX /usr/local/miniconda; sync && \
+    chmod +x /usr/local/miniconda/bin/*; sync && \
+    conda clean -y --all; sync && \
+    conda clean -tipsy; sync && \
+    rm -rf ~/.conda ~/.cache/pip/*; sync
+
 RUN apt-get update && \
     DEBIAN_FRONTEND=noninteractive \
     apt-get install -y --no-install-recommends \
-                    afni=18.0.05+git24-gb25b21054~dfsg.1-1~nd17.10+1+nd18.04+1 \
-                    connectome-workbench=1.5.0-1~nd18.04+1 \
-                    git-annex-standalone && \
+        afni=18.0.05+git24-gb25b21054~dfsg.1-1~nd17.10+1+nd18.04+1 \
+        connectome-workbench=1.5.0-1~nd18.04+1 \
+        git-annex-standalone && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+# Install 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 \
     --exclude='freesurfer/diffusion' \
     --exclude='freesurfer/docs' \
@@ -69,80 +104,46 @@ 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 FSF_OUTPUT_FORMAT="nii.gz" \
-    FREESURFER_HOME="/opt/freesurfer"
-
-ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+ENV FREESURFER_HOME="/opt/freesurfer" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
     FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
-    MNI_DIR="$FREESURFER_HOME/mni" \
     LOCAL_DIR="$FREESURFER_HOME/local" \
     MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
     MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
     MNI_DATAPATH="$FREESURFER_HOME/mni/data"
-
-ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
     MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
+    SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
     PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
 
 ENV 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/afni/bin:$PATH"
+    AFNI_PLUGINPATH="/usr/lib/afni/plugins" \
+    PATH="/usr/lib/afni/bin:$PATH"
 
-
-ENV ANTSPATH=/usr/lib/ants
+# Install ANTS
+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" \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH:$PATH
 
-# Installing SVGO
+# Install SVGO
 RUN curl -sL https://deb.nodesource.com/setup_14.x | bash -
 RUN apt-get install -y nodejs
 RUN npm install -g svgo
 
-# Installing bids-validator
+# Install bids-validator
 RUN npm install -g [email protected]
 
-# 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 && \
-    rm Miniconda3-py38_4.9.2-Linux-x86_64.sh
-
-# 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" \
-    LANG="C.UTF-8" \
-    LC_ALL="C.UTF-8" \
-    PYTHONNOUSERSITE=1
-
-# Installing precomputed python packages
-RUN conda install -y python=3.8 \
-                     pip=21.0 \
-                     mkl=2021.2 \
-                     mkl-service=2.3 \
-                     numpy=1.18.1 \
-                     scipy=1.6 \
-                     scikit-learn=0.24 \
-                     matplotlib=3.3 \
-                     pandas=1.2 \
-                     libxslt=1.1 \
-                     traits=6.2 \
-                     zstd=1.4; 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
-#RUN pip install numpy==1.18.1
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
 # Create a shared $HOME directory
-
 RUN useradd -m -s /bin/bash -G users xcp_d
 WORKDIR /home/xcp_d
 ENV HOME="/home/xcp_d"
@@ -152,7 +153,7 @@ RUN python -c "from matplotlib import font_manager" && \
     sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
 
 # Precaching atlases: UPDATE TEMPLATEFLOW VERSION TO MATCH XCP_D
-RUN pip install --no-cache-dir "templateflow ~= 0.6.1 " && \
+RUN pip install --no-cache-dir "templateflow ~= 0.8.1 " && \
     python -c "from templateflow import api as tfapi; \
                tfapi.get('MNI152NLin2009cAsym', resolution=2, suffix='T1w', desc=None); \
                 tfapi.get(template='MNI152NLin6Asym',resolution=2, suffix='T1w'); \