seunglab/synaptor repository overview

FROM nvidia/cuda:8.0-cudnn6-devel-ubuntu16.04

#Setting up ENV RUN echo "deb http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64⁠ /" > /etc/apt/sources.list.d/nvidia-ml.list

ENV PYTHON_VERSION=3.6 ENV PATH /opt/conda/bin:$PATH

RUN apt-get update &&
pytorchDeps='build-essential cmake git vim ca-certificates libnccl2=2.0.5-2+cuda8.0 libnccl-dev=2.0.5-2+cuda8.0' &&
igraphDeps='libxml2-dev zlib1g-dev pkg-config libffi-dev libcairo-dev' &&
condaDeps='wget bzip2 libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion' &&
apt-get install -y --no-install-recommends $pytorchDeps $igraphDeps $condaDeps &&
rm -rf /var/lib/apt/lists/* &&
#Install miniconda3 echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh &&
wget --quiet https://repo.continuum.io/miniconda/Miniconda3-4.3.27-Linux-x86_64.sh⁠ -O ~/miniconda.sh &&
/bin/bash ~/miniconda.sh -b -p /opt/conda &&
rm ~/miniconda.sh &&
#Fixes a conda bug - https://github.com/conda/conda/issues/6030⁠ conda update python &&
#Python Dependencies #For some reason, pip works for h5py and pandas, and conda doesn't pip --no-cache-dir install h5py pandas cloud-volume python-igraph &&
conda install scipy pytorch torchvision -c pytorch &&
git clone https://github.com/nicholasturner1/Synaptor.git⁠ &&
pip install -e /Synaptor &&
conda clean -t -p &&
apt-get purge -y --auto-remove $pytorchDeps $condaDeps #$igraphDeps #need these

WORKDIR /Synaptor/tasks ENTRYPOINT ["bash","dispatcher.sh"]