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python/docker/Dockerfile

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+# Generated by Neurodocker and Reproenv.
+
+FROM pyushkevich/itksnap:v3.8.2
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update -qq \
+           && apt-get install -y -q --no-install-recommends \
+                  emacs-nox \
+                  g++ \
+                  gcc \
+                  graphviz \
+                  less \
+                  nano \
+                  ncdu \
+                  netbase \
+                  tig \
+                  tree \
+                  vim \
+                  make \
+                  cmake \
+           && rm -rf /var/lib/apt/lists/*
+
+# install ANTs
+
+RUN curl -o installANTs.sh https://raw.githubusercontent.com/cookpa/antsInstallExample/master/installANTs.sh
+
+RUN bash installANTs.sh
+
+# RUN export PATH=/app/install/bin:$PATH
+
+ENV PATH /app/install/bin:$PATH
+
+# Update other required stuff
+
+RUN export TMPDIR="$(mktemp -d)" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           ca-certificates \
+           curl \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* 
+
+
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           ca-certificates \
+           curl \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libgl1-mesa-dri \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libopenblas-base \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           nano \
+           sudo \
+           wget \
+    && rm -rf /var/lib/apt/lists/* 
+
+
+# Set up anaconda
+ENV CONDA_DIR="/opt/miniconda-4.7.12" \
+    PATH="/opt/miniconda-4.7.12/bin:$PATH"
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bzip2 \
+           ca-certificates \
+           curl \
+    && rm -rf /var/lib/apt/lists/* \
+    # Install dependencies.
+    && export PATH="/opt/miniconda-4.7.12/bin:$PATH" \
+    && echo "Downloading Miniconda installer ..." \
+    && conda_installer="/tmp/miniconda.sh" \
+    && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-4.7.12-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-4.7.12 \
+    && rm -f "$conda_installer" \
+    # Prefer packages in conda-forge
+    && conda config --system --prepend channels conda-forge \
+    # Packages in lower-priority channels not considered if a package with the same
+    # name exists in a higher priority channel. Can dramatically speed up installations.
+    # Conda recommends this as a default
+    # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
+    && conda config --set channel_priority strict \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    # Enable `conda activate`
+    && conda init bash 
+
+
+
+# install FSL
+
+
+# store the FSL public conda channel
+ENV FSL_CONDA_CHANNEL="https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public"
+
+# install tini into base conda environment
+RUN /opt/miniconda-4.7.12/bin/conda install -n base -c conda-forge tini
+# as a demonstration, install ONLY FSL's bet (brain extraction) tool. This is an example of a minimal, yet usable container without the rest of FSL being installed
+# to see all packages available use a browser to navigate to: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
+# note the channel priority. The FSL conda channel must be first, then condaforge
+RUN /opt/miniconda-4.7.12/bin/conda install -n base -c $FSL_CONDA_CHANNEL fsl-flirt fsl-bet2 -c conda-forge
+# set FSLDIR so FSL tools can use it, in this minimal case, the FSLDIR will be the root conda directory
+ENV FSLDIR="/opt/miniconda-4.7.12"
+ENV FSLOUTPUTTYPE="NIFTI_GZ"
+
+# install the python requirements for iEEG-recon
+RUN pip install --upgrade pip
+
+# Install any dependencies specified in requirements.txt
+RUN pip install --no-cache-dir ipython\
+ nibabel\
+ numpy\
+ pandas\
+ plotly\
+ nipype\
+ niworkflows\
+ antspyx\
+ antspynet\
+ pyqt5\
+ pydeface
+
+# RUN git clone https://github.com/ANTsX/ANTsPy && cd ANTsPy && python3 setup.py install
+
+
+RUN mkdir /code && chmod 777 /code && chmod a+rwx /code
+
+RUN mkdir /code/voxtool && chmod 777 /code/voxtool && chmod a+rwx /code/voxtool
+
+# Create placeholder files
+RUN mkdir /atlas_files && chmod 777 /atlas_files && chmod a+rwx /atlas_files
+RUN touch /atlas_files/labels.txt
+RUN touch /atlas_files/indices.txt
+RUN touch /atlas_files/atlas.nii.gz
+RUN touch /atlas_files/lut.txt
+
+
+RUN mkdir /freesurfer && chmod 777 /freesurfer && chmod a+rwx /freesurfer
+
+RUN mkdir /source_data && chmod 777 /source_data && chmod a+rwx /source_data
+RUN mkdir /outputs && chmod 777 /outputs && chmod a+rwx /outputs
+
+
+ENV PATH="${PATH}:/code"
+#ENV PATH="/code:$PATH"
+
+RUN test "$(getent passwd neuro)" \
+    || useradd --no-user-group --create-home --shell /bin/bash neuro
+
+
+# Download the ieeg-recon repository and then copy the appropriate scripts/files to the appropriate folders
+RUN mkdir /opt/ieeg_recon \
+  && cd /opt/ieeg_recon \
+  && git clone https://github.com/penn-cnt/ieeg-recon.git
+
+# Copy the main scripts from the repository folder to the code folder
+
+RUN cp /opt/ieeg_recon/ieeg_recon/python/docker/ieeg_recon_main_docker.py /code/ieeg_recon_v2.py \
+  && cp /opt/ieeg_recon/ieeg_recon/python/pipeline/* /code \
+  && cp /opt/ieeg_recon/ieeg_recon/python/reports/* /code \
+  && cp /opt/ieeg_recon/ieeg_recon/python/source_data/* /code \
+  && cp /opt/ieeg_recon/ieeg_recon/python/docker/brain_shift.py /code 
+  # the brain shift code is different
+
+RUN chmod +x /code/ieeg_recon_v2.py
+
+ENTRYPOINT ["python","/code/ieeg_recon_v2.py"]
+
+