pykilosort container - initial version

Author: vncntprvst

pykilosort/Dockerfile

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+FROM nvidia/cuda:10.0-base-ubuntu18.04 
+
+LABEL maintainer="Vincent Prevosto <prevosto@mit.edu>"
+
+# USER root
+# # Ubuntu package installs
+RUN apt update 
+RUN apt install -y --no-install-recommends \
+    libfftw3-dev \
+    git \
+    wget && \
+    apt clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Make bash the default shell, for compatibility with conda
+# SHELL [ "/bin/bash", "--login",  "-c" ]
+
+# install miniconda
+ENV MINICONDA_VERSION 4.12.0
+ENV CONDA_DIR /home/miniconda3
+ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
+
+RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
+    bash ~/miniconda.sh -b -p $CONDA_DIR && \
+    rm ~/miniconda.sh
+# RUN echo 'export PATH="~/miniconda/bin:$PATH"' >> ~/.bashrc 
+ENV PATH=$CONDA_DIR/bin:$PATH
+RUN conda update conda
+
+# chmod +x ~/miniconda.sh && \
+# ~/miniconda.sh -b -p $CONDA_DIR && \
+# rm ~/miniconda.sh
+
+# # make non-activate conda commands available
+# ENV PATH=$CONDA_DIR/bin:$PATH
+# # make conda activate command available from /bin/bash --login shells
+# RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> /root/.profile 
+# # make conda activate command available from /bin/bash --interactive shells
+# RUN conda init bash
+
+# Install IBL port of pykilosort
+RUN git clone -b drift_test_stable https://github.com/kushbanga/pykilosort.git /src/pykilosort
+WORKDIR /src/pykilosort
+
+# Create environment
+RUN conda env create -f pyks2.yml
+
+# Install pykilosort
+SHELL ["conda","run","-n","pyks2","/bin/bash","-c"]
+# RUN conda install --quiet --yes ipykernel && \
+#     python -m ipykernel install --user --name pyks2 --display-name "pyKilosort" && \
+RUN conda develop .
+
+
+
+

pykilosort/build.sh

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+#!/bin/bash
+
+docker build -t spikeinterface/pykilosort:0.1.0 .

pykilosort/push.sh

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+#!/bin/bash
+
+docker push -t spikeinterface/pykilosort:0.1.0 .