Dockerfile

# Generated by Neurodocker v0.3.2.
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#     https://github.com/kaczmarj/neurodocker
#
# Timestamp: 2018-02-02 16:32:55

FROM debian:stretch

ARG DEBIAN_FRONTEND=noninteractive

#----------------------------------------------------------
# Install common dependencies and create default entrypoint
#----------------------------------------------------------
# replace shell with bash so we can source files
RUN rm /bin/sh && ln -s /bin/bash /bin/sh


ENV LANG="en_US.UTF-8" \
    LC_ALL="C.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"

RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
    	apt-utils \
        bzip2 \
        ca-certificates \
        cmake \
        curl \
        dirmngr \
        g++ \
        gcc \
        git \
        gnupg \
        locales \
        make \
        nano \
        pigz \
        unzip \
        zlib1g-dev \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
    && localedef --force --inputfile=en_US --charmap=UTF-8 C.UTF-8 \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> $ND_ENTRYPOINT \
         && echo 'set +x' >> $ND_ENTRYPOINT \
         && echo 'if [ -z "$*" ]; then /usr/bin/env bash; else $*; fi' >> $ND_ENTRYPOINT; \
       fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

#-------------------------------
# Install dcm2niix v1.0.20200331
#-------------------------------
RUN mkdir -p /src/dcm2niix \
    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20200331 | tar xz -C /src/dcm2niix --strip-components 1 \
    && mkdir /src/dcm2niix/build && cd /src/dcm2niix/build \
    && cmake .. && make \
    && make install

#--------------------------------------------------
# Add NeuroDebian repository
# Please note that some packages downloaded through
# NeuroDebian may have restrictive licenses.
#--------------------------------------------------
RUN curl -sSL http://neuro.debian.net/lists/stretch.us-nh.full \
    > /etc/apt/sources.list.d/neurodebian.sources.list \
    && curl -sSL https://dl.dropbox.com/s/zxs209o955q6vkg/neurodebian.gpg \
    | apt-key add - \
    && (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 || true) \
    && apt-get update

#----------------------------------
# Install Datalad (via NeuroDebian)
#----------------------------------
RUN apt-get update -qq && apt-get install -yq --no-install-recommends \
        datalad \
        git-annex-standalone \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

#--------------------
# Download mri_deface
#--------------------
# Download mri_deface nd additional files from MGH
USER root
ENV DEFACE_DIR /src/deface
RUN mkdir -p $DEFACE_DIR

RUN curl -sSL -o $DEFACE_DIR/mri_deface \
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/mri_deface_linux && \
  chmod +x $DEFACE_DIR/mri_deface

RUN curl -sSL -o $DEFACE_DIR/face.gca.gz \
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/face.gca.gz && \
  gunzip $DEFACE_DIR/face.gca.gz

RUN curl -sSL -o $DEFACE_DIR/talairach_mixed_with_skull.gca.gz \
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_deface/talairach_mixed_with_skull.gca.gz && \
  gunzip $DEFACE_DIR/talairach_mixed_with_skull.gca.gz

ENV PATH=$PATH:$DEFACE_DIR

#---------------
# BIDS-validator
#---------------
#Install nvm
ENV NVM_DIR /usr/local/nvm
ENV NODE_VERSION 10.16.3

# https://github.com/creationix/nvm#install-script
RUN curl --silent -o- https://raw.githubusercontent.com/creationix/nvm/v0.31.2/install.sh | bash

# install node and npm
RUN source $NVM_DIR/nvm.sh \
    && nvm install $NODE_VERSION \
    && nvm alias default $NODE_VERSION \
    && nvm use default

# add node and npm to path so the commands are available
ENV NODE_PATH $NVM_DIR/v$NODE_VERSION/lib/node_modules
ENV PATH $NVM_DIR/versions/node/v$NODE_VERSION/bin:$PATH

RUN npm install -g bids-validator@1.5.4

#---------------------
# Create neuro account
#---------------------
RUN useradd --no-user-group --create-home --shell /bin/bash neuro

USER neuro

WORKDIR /home/neuro

#------------------
# Install Miniconda
#------------------
ENV CONDA_DIR=/opt/conda \
    PATH=/opt/conda/bin:$PATH
RUN echo "Downloading Miniconda installer ..." \
    && miniconda_installer=/tmp/miniconda.sh \
    && curl -sSL --retry 5 -o $miniconda_installer https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && /bin/bash $miniconda_installer -b -p $CONDA_DIR \
    && rm -f $miniconda_installer \
    && conda update -yq -nbase conda \
    && conda config --system --prepend channels conda-forge \
    && conda config --system --set auto_update_conda false \
    && conda config --system --set show_channel_urls true \
    && conda clean -tipsy && sync

#-------------------------
# Create conda environment
#-------------------------
COPY [".", "/src/bidsify"]
USER root
RUN chmod 755 -R /src/
RUN conda create -y -q --name neuro python=3.7 \
    && sync && conda clean --all && sync \
    && /bin/bash -c "source activate neuro \
          && pip install /src/bidsify/"\
    && sync \
    && sed -i '$isource activate neuro' $ND_ENTRYPOINT

USER root

RUN mkdir /work && chown -R neuro /src /work

USER neuro

RUN bash -c "source activate neuro \
    && pip install --no-cache-dir /src/bidsify/" \
    && rm -rf ~/.cache/pip/* \
    && sync

#----------------------
# Set entrypoint script
#----------------------
ENTRYPOINT ["/neurodocker/startup.sh", "bidsify"]

#--------------------------------------------
# Set environmental variables for Singularity
#--------------------------------------------
ENV SINGULARITY_CACHEDIR /scratch
ENV SINGULARITY_TMPDIR /scratch

#-------------------------------
# Set user and working directory
#-------------------------------
USER neuro
WORKDIR /work