tractify/Dockerfile at master · TIGRLab/tractify · GitHub

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FROM vnmd/mrtrix3_3.0.2:latest

USER root

# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-linux-centos8_x86_64-7.1.0.tar.gz \
    | tar zxv --no-same-owner -C /opt \
    --exclude='freesurfer/diffusion' \
    --exclude='freesurfer/docs' \
    --exclude='freesurfer/fsfast' \
    --exclude='freesurfer/lib/cuda' \
    --exclude='freesurfer/lib/qt' \
    --exclude='freesurfer/matlab' \
    --exclude='freesurfer/mni/share/man' \
    --exclude='freesurfer/subjects/fsaverage_sym' \
    --exclude='freesurfer/subjects/fsaverage3' \
    --exclude='freesurfer/subjects/fsaverage4' \
    --exclude='freesurfer/subjects/cvs_avg35' \
    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
    --exclude='freesurfer/subjects/bert' \
    --exclude='freesurfer/subjects/lh.EC_average' \
    --exclude='freesurfer/subjects/rh.EC_average' \
    --exclude='freesurfer/subjects/sample-*.mgz' \
    --exclude='freesurfer/subjects/V1_average' \
    --exclude='freesurfer/trctrain'

# Simulate SetUpFreeSurfer.sh
ENV FSL_DIR="/opt/fsl-6.0.1" \
    OS="Linux" \
    FS_OVERRIDE=0 \
    FIX_VERTEX_AREA="" \
    FSF_OUTPUT_FORMAT="nii.gz" \
    FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
    FUNCTIONALS_DIR="$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_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$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 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

# 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

# Add credentials on build
RUN mkdir ~/.ssh && ln -s /run/secrets/host_ssh_key ~/.ssh/id_rsa

RUN conda install -y python=3.7.3 \
                     pip=19.1 \
                     libxml2=2.9.8 \
                     libxslt=1.1.32 \
                     graphviz=2.40.1; 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

RUN pip install --upgrade pip

#RUN mkdir tractify
#COPY ./ tractify/
#RUN cd tractify && pip install .

RUN git clone https://github.com/TIGRLab/tractify /tractify && \
    pip install packaging==23.1 dipy==1.6.0 && \
    cd /tractify && \
    pip install .

ENTRYPOINT ["tractify"]