Removes "add main user" from dockerfile - not needed for mybinder.org

Dockerfile

@@ -1,17 +1,102 @@
-# This Dockerfile is based on 'miykael/nipype_env', for more information see:
-# https://hub.docker.com/r/miykael/nipype_env/
+# This Dockerfile is based on the dockerfiles 'crn_base' and 'crn_nipype' from
+# the Poldrack Lab (https://github.com/poldracklab/crn_base), the dockerfiles
+# from neurovault (https://github.com/NeuroVault/NeuroVault) and the dockerfile
+# biss2016-notebook from Oscar Esteban under https://hub.docker.com/u/oesteban.
+#
+# This means that the same copyrights apply to this Dockerfile, as they do for
+# the above mentioned dockerfiles. For more information see:
+# https://github.com/miykael/nipype_env
 
-FROM miykael/nipype_env
 MAINTAINER Michael Notter <michaelnotter@hotmail.com>
 
-# Switch to root user
+# Switch to root user for installation
 USER root
 
-# Create main user and home folder
-RUN useradd -ms /bin/bash main
-USER main
-WORKDIR /home/main
+# Preparations
+RUN ln -snf /bin/bash /bin/sh
+ARG DEBIAN_FRONTEND=noninteractive
 
-#RUN find $HOME/notebooks -name '*.ipynb' -exec ipython trust {} \;
+# Update packages and install the minimal set of tools
+RUN apt-get update && \
+    apt-get install -y curl \
+                       git \
+                       xvfb \
+                       bzip2 \
+                       unzip \
+                       apt-utils \
+                       gfortran \
+                       fusefat \
+                       liblapack-dev \
+                       libblas-dev \
+                       libatlas-dev \
+                       libatlas-base-dev \
+                       libblas3 \
+                       libblas-common \
+                       libopenblas-dev \
+                       libxml2-dev \
+                       libxslt1-dev \
+                       libfreetype6-dev \
+                       libpng12-dev \
+                       libqhull-dev \
+                       libxft-dev \
+                       libjpeg-dev \
+                       libyaml-dev -qq
+
+# Enable neurodebian
+RUN curl -sSL http://neuro.debian.net/lists/jessie.de-md.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
+    curl -sSL http://neuro.debian.net/lists/jessie.us-tn.full >> /etc/apt/sources.list.d/neurodebian.sources.list
+RUN apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
+RUN apt-get update -qq
+RUN apt-get install -y fsl afni -qq
+
+# Set-up environment
+RUN echo '#!/bin/bash' > /etc/profile.d/neuro_env.sh && \
+    echo 'FSLDIR=/usr/share/fsl' >> /etc/profile.d/neuro_env.sh && \
+    echo 'source /etc/fsl/fsl.sh' >> /etc/profile.d/neuro_env.sh && \
+    echo 'PATH=$FSLDIR/5.0/bin:$PATH' >> /etc/profile.d/neuro_env.sh && \
+    echo 'export FSLDIR PATH' >> /etc/profile.d/neuro_env.sh && \
+    echo 'export PATH=/usr/lib/afni/bin:$PATH' >> /etc/profile.d/neuro_env.sh && \
+    echo 'source /etc/profile.d/neuro_env.sh' >> /etc/bash.bashrc
+#RUN source activate neuro_env
+
+# Update conda and install relevant dependencies
+RUN conda update conda --yes --quiet
+RUN conda update anaconda --yes --quiet
+RUN conda install --yes --quiet cython \
+                        h5py \
+                        ipython \
+                        jupyter \
+                        matplotlib \
+                        networkx \
+                        nose \
+                        numpy \
+                        pandas \
+                        scikit-image \
+                        scikit-learn \
+                        scipy \
+                        seaborn
+RUN python -c "from matplotlib import font_manager"
+RUN conda clean -a
+
+# Install dependencies in pip
+RUN pip install --upgrade pip && \
+    pip install --upgrade dipy \
+                          graphviz \
+                          nibabel \
+                          nipy \
+                          pydotplus \
+                          rdflib \
+                          xvfbwrapper \
+                --ignore-installed
+
+# Install nipype
+RUN pip install -e git+https://github.com/nipy/nipype#egg=nipype
+
+# Clear apt cache and other empty folders
+RUN apt-get clean remove -y && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    rm -rf /boot /media /mnt /opt /srv
 
 ENV SHELL /bin/bash
+
+CMD ["/bin/bash"]

README.md

@@ -1,10 +1,17 @@
 # Nipype Tutorial Notebooks
 
-The Nipype tutorial notebooks run on [mybinder.org](http://mybinder.org/) and can be started by clicking on the following button: [![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/miykael/nipype_notebooks)
+The Nipype tutorial runs on [mybinder.org](http://mybinder.org/) and can be started by clicking on the following button: [![Binder](http://mybinder.org/badge.svg)](http://mybinder.org/repo/miykael/nipype_tutorial)
+
+The Dockerfile that creates the nipype environment on mybinder is based on the docker image [miykael/nipype_basic](https://hub.docker.com/r/miykael/nipype_basic/).
 
 
 ## The Dataset
 
 The data used for this tutorial is from [openfmri.org](https://openfmri.org/) and is structured according the new and fancy [Brain Imaging Data Structure (BIDS)](http://bids.neuroimaging.io/).
 
 The dataset ds005 used for this tutorial was shortened to only two subjects, *sub-15* and *sub-16* and restricted to the first two functional runs. For more information about the dataset, see the [description on openfmri.org](https://openfmri.org/dataset/ds000105/).
+
+
+## Feedback, Help & Support
+
+If you want to help us with this tutorial or have any questions, fell free to fork our repo [github.com/miykael/nipype_tutorial](https://github.com/miykael/nipype_tutorial) or interact with other contributors on the slack channel [brainhack.slack.com/messages/nipype/](https://brainhack.slack.com/messages/nipype/)

example_nb/mwaskom/Makefile

@@ -0,0 +1,5 @@
+.PHONY: clean
+
+clean:
+	@-rm -rf *.nii* data/T1*_*.nii* data/timeseries_*.nii.* data/*.nii\
+         crash-* *.dot* working_dir/ smoothflow/ susanflow/

example_nb/mwaskom/README.md

@@ -0,0 +1,27 @@
+Nipype Concepts
+===============
+
+This collection of [IPython](http://ipython.org/)
+notebooks should provide an introduction to some of the 
+main concepts central to using [Nipype](http://nipy.sourceforge.net/nipype/)
+for neuroimaging analysis. 
+
+Static HTML Links
+-----------------
+
+- [Interfaces](http://nbviewer.ipython.org/urls/raw.github.com/mwaskom/nipype_concepts/master/interfaces.ipynb)
+- [Workflows](http://nbviewer.ipython.org/urls/raw.github.com/mwaskom/nipype_concepts/master/workflows.ipynb)
+- [Iteration](http://nbviewer.ipython.org/urls/raw.github.com/mwaskom/nipype_concepts/master/iteration.ipynb)
+
+Requirements
+------------
+
+- [IPython](http://ipython.org/)
+- [Nipype](http://nipy.sourceforge.net/nipype/)
+- [FSL](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
+- [SPM](http://www.fil.ion.ucl.ac.uk/spm/) (Optional)
+
+License
+-------
+
+Simplified BSD