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Updated Dockerfile #209

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4c84149
added installation of apt-transport-https after nvidia docker file up…
May 10, 2018
ada3804
Fixed dockerfile issues
May 14, 2018
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26 changes: 15 additions & 11 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@ FROM nvidia/cuda:9.1-cudnn7-devel-ubuntu16.04 AS nvidia

FROM continuumio/anaconda3:5.0.1

RUN apt-get update && apt-get install apt-transport-https


COPY --from=nvidia /etc/apt/sources.list.d/cuda.list /etc/apt/sources.list.d/
COPY --from=nvidia /etc/apt/sources.list.d/nvidia-ml.list /etc/apt/sources.list.d/
COPY --from=nvidia /etc/apt/trusted.gpg /etc/apt/trusted.gpg.d/cuda.gpg
Expand Down Expand Up @@ -49,7 +52,7 @@ RUN sed -i "s/httpredir.debian.org/debian.uchicago.edu/" /etc/apt/sources.list &
pip install scipy --upgrade && \
pip install seaborn python-dateutil dask pytagcloud pyyaml joblib \
husl geopy ml_metrics mne pyshp gensim && \
conda install -y -c conda-forge spacy && python -m spacy download en && \
pip install spacy && python -m spacy download en && \
python -m spacy download en_core_web_lg && \
# The apt-get version of imagemagick is out of date and has compatibility issues, so we build from source
apt-get -y install dbus fontconfig fontconfig-config fonts-dejavu-core fonts-droid ghostscript gsfonts hicolor-icon-theme \
Expand Down Expand Up @@ -155,7 +158,7 @@ RUN apt-get install -y libfreetype6-dev && \
echo "x" > README.rst && echo "x" > CHANGES.rst && \
python setup.py install && \
# Dev branch of Theano
pip install git+git://github.com/Theano/Theano.git --upgrade --no-deps && \
pip install https://github.com/Theano/Theano/archive/rel-0.8.2.zip --upgrade --no-deps && \
# put theano compiledir inside /tmp (it needs to be in writable dir)
printf "[global]\nbase_compiledir = /tmp/.theano\n" > /.theanorc && \
cd /usr/local/src && git clone --depth 1 https://github.com/pybrain/pybrain && \
Expand Down Expand Up @@ -196,14 +199,14 @@ vader_lexicon verbnet webtext word2vec_sample wordnet wordnet_ic words ycoe && \
# Make sure the dynamic linker finds the right libstdc++
ENV LD_LIBRARY_PATH="/opt/conda/lib:${LD_LIBRARY_PATH}"

#RUN pip install --upgrade pip setuptools

RUN apt-get update && \
# Libgeos, for mapping libraries
apt-get -y install libgeos-dev && \
# pyshp and pyproj are now external dependencies of Basemap
pip install pyshp pyproj && \
cd /usr/local/src && git clone https://github.com/matplotlib/basemap.git && \
export GEOS_DIR=/usr/local && \
cd basemap && python setup.py install && \
conda install -c conda-forge basemap && \
# Pillow (PIL)
apt-get -y install zlib1g-dev liblcms2-dev libwebp-dev && \
pip install Pillow && \
Expand Down Expand Up @@ -245,9 +248,7 @@ RUN apt-get update && \
python -c "from keras.models import Sequential; from keras import backend; print(backend._BACKEND)" && \
# Keras reverts to /tmp from ~ when it detects a read-only file system
mkdir -p /tmp/.keras && cp /root/.keras/keras.json /tmp/.keras && \
# Scikit-Learn nightly build
cd /usr/local/src && git clone https://github.com/scikit-learn/scikit-learn.git && \
cd scikit-learn && python setup.py build && python setup.py install && \
pip install scikit-learn && \
# HDF5 support
conda install h5py && \
# https://github.com/biopython/biopython
Expand Down Expand Up @@ -282,13 +283,15 @@ RUN apt-get update && \
#./waf && ./waf install && mv /usr/local/lib/python3.6/site-packages/essentia /opt/conda/lib/python3.6 && \
# Install torch and torchvision from source, so we're using the cuda/cudnn libraries installed above.
conda install mkl setuptools cmake cffi typing && \
#mkl-include is needed to compile pytorch
conda install mkl-include && \
conda install -c pytorch magma-cuda90 && \
cd /usr/local/src && \
git clone -b v0.3.1 --recursive https://github.com/pytorch/pytorch && \
git clone -b v0.4.0 --recursive https://github.com/pytorch/pytorch && \
cd pytorch && \
python setup.py install && \
cd /usr/local/src && \
git clone -b v0.2.0 --recursive https://github.com/pytorch/vision && \
git clone -b v0.2.1 --recursive https://github.com/pytorch/vision && \
cd vision && \
python setup.py install && \
# PyTorch Audio
Expand Down Expand Up @@ -359,7 +362,7 @@ RUN pip install --upgrade mpld3 && \
conda install -y ecos && \
conda install -y CVXcanon && \
pip install fancyimpute && \
pip install git+https://github.com/pymc-devs/pymc3 && \
pip install https://github.com/pymc-devs/pymc3/archive/v3.0.zip && \
pip install tifffile && \
pip install spectral && \
pip install descartes && \
Expand Down Expand Up @@ -463,6 +466,7 @@ RUN pip install --upgrade cython && \
# clean up pip cache
rm -rf /root/.cache/pip/* && \
# Required to display Altair charts in Jupyter notebook
pip install vega && \
jupyter nbextension install --user --py vega

# Fast.ai and dependencies
Expand Down