anchor.diff: -# Generated by Neurodocker v0.2.0-30-g4b9bd64.
  +# Generated by Neurodocker v0.3.1-19-g8d02eb4.
   #
  -# Thank you for using Neurodocker. If you discover any issues 
  -# or ways to improve this software, please submit an issue or 
  +# 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: 2017-09-06 14:26:38
  +# Timestamp: 2017-11-03 19:55:05
   
   FROM neurodebian:stretch-non-free
   
  
positive.code:     \n        "less", \
      \n        "ncdu", \
      \n        "tig", \
      \n        "git-annex-remote-rclone", \
      \n        "build-essential", \
      \n        "nodejs", \
      \n        "r-recommended", \
      \n        "psmisc", \
      \n        "libapparmor1", \
      \n        "sudo", \
      \n        "dc" \
      \n      ] \
      \n    ], \
      \n    [ \
      \n      "install", \
      \n      [ \
      \n        "afni" \
      \n      ] \
      \n    ], \
      \n    [ \
      \n      "instruction", \
      \n      "ENV PATH=/usr/lib/afni/bin:$PATH " \
      \n    ], \
      \n    [ \
      \n      "freesurfer", \
      \n      { \
      \n        "version": "6.0.0", \
      \n        "min": true \
      \n      } \
      \n    ], \
      \n    [ \
      \n      "install", \
      \n      [ \
      \n        "fsl" \
      \n      ] \
      \n    ], \
      \n    [ \
      \n      "instruction", \
      \n      "RUN sed -i '$iFSLDIR=/usr/share/fsl\\n. ${FSLDIR}/5.0/etc/fslconf/fsl.sh\\nPATH=${FSLDIR}/5.0/bin:${PATH}\\nexport FSLDIR PATH' $ND_ENTRYPOINT" \
      \n    ], \
      \n    [ \
      \n      "spm", \
  
negative.code:     && 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
  #-------------------------
  RUN conda create -y -q --name neuro python=3.6 \
                                      jupyter \
                                      jupyterlab \
                                      jupyter_contrib_nbextensions \
                                      traits \
                                      pandas \
                                      matplotlib \
                                      scikit-learn \
                                      seaborn \
                                      swig \
                                      reprozip \
                                      reprounzip \
      && sync && conda clean -tipsy && sync \
      && /bin/bash -c "source activate neuro \
        && pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master \
                                         https://github.com/INCF/pybids/tarball/master \
                                         nilearn \
                                         datalad[full] \
                                         dipy \
                                         nipy \
                                         duecredit \
                                         pymvpa2" \
      && sync \
      && sed -i '$isource activate neuro' $ND_ENTRYPOINT
  
  # User-defined BASH instruction
  RUN bash -c "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main"
  
  # User-defined instruction
  RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
  
  COPY [".", "/home/neuro/"]
  
  USER root
  
  # User-defined instruction
  RUN chown -R neuro /home/neuro
  
  # User-defined instruction
  RUN mkdir /data && chmod 777 /data && chmod a+s /data
  
  # User-defined instruction
  RUN mkdir /output && chmod 777 /output && chmod a+s /output
  
  USER neuro
  
  # User-defined BASH instruction
  RUN bash -c "source activate neuro && cd	/data && datalad install -r ///workshops/nih-2017/ds000114 \
      && cd /data/ds000114 && datalad get sub-*/ses-test/anat && datalad get sub-*/ses-test/func/*fingerfootlips* && datalad get derivatives/fmriprep/sub-*/anat && datalad get derivatives/fmriprep/sub-*/ses-test/func/*fingerfootlips*"
  
  WORKDIR /home/neuro
  
  CMD ["jupyter-notebook"]
  
  #--------------------------------------
  # Save container specifications to JSON
  