Merge pull request #9 from int-brain-lab/main

Yass dockerfile

Author: alejoe91

yass/Dockerfile

@@ -0,0 +1,54 @@
+#docker build -t ibl/yass:base .
+FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04
+
+# link the cuda libraries
+ENV LD_LIBRARY_PATH /usr/local/cuda/extras/CUPTI/lib64:$LD_LIBRARY_PATH
+
+# setup time zone for tz
+ENV TZ=Europe/Paris
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# Install python3.7
+RUN apt-get update
+RUN apt-get install -y software-properties-common wget
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update
+RUN apt-get install -y python3.7 python3.7-dev python3.7-tk python3-pip python3.7-venv git ffmpeg libgtk-3-dev
+
+# Install Python dependencies
+ARG PYTHON=python3.7
+ENV LANG C.UTF-8
+ENV CONDA_PATH=/opt/anaconda3
+ENV ENVIRONMENT_NAME=main
+SHELL ["/bin/bash", "-c"]
+
+# Download and install Anaconda.
+ENV LATEST_CONDA_SCRIPT "Anaconda3-5.3.1-Linux-x86_64.sh"
+ENV PATH="/root/anaconda2/bin:${PATH}"
+
+RUN wget https://repo.continuum.io/archive/$LATEST_CONDA_SCRIPT
+
+RUN bash $LATEST_CONDA_SCRIPT -b -p /home/anaconda3 \
+	&& echo "export PATH=/home/anaconda/bin:$PATH" >> ~/.bashrc \
+	&& /bin/bash -c "source /root/.bashrc"
+
+ENV PATH /home/anaconda3/bin:$PATH
+
+RUN conda install pytorch==1.2
+#RUN rm $LATEST_CONDA_SCRIPT
+#conda install pytorch==1.2.0 torchvision==0.4.0 cudatoolkit=10.0 -c pytorch
+
+RUN git clone https://github.com/paninski-lab/yass \
+   && cd yass \
+   && pip --no-cache-dir install -e . \
+   && cd src/gpu_bspline_interp \
+   && python setup.py install --force \
+   && cd .. \
+   && cd gpu_rowshift \
+   && python setup.py install --force \
+   && cd ../.. \
+   && pip install .
+
+RUN pip install scipy==1.2.0
+#cd yass/samples/10chan
+#yass sort config.yaml