Merge pull request #2 from SpikeInterface/kilosort3

add kilosort3 docker image

Author: samuelgarcia

kilosort3/Dockerfile

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+FROM magland/matlab_for_kilosort:0.1.0
+
+#########################################
+### Python                                                               
+RUN apt update && apt -y install git wget build-essential
+RUN apt install -y python3 python3-pip
+RUN rm -f /usr/bin/python && ln -s python3 /usr/bin/python
+RUN rm -f /usr/bin/pip && ln -s pip3 /usr/bin/pip
+RUN DEBIAN_FRONTEND=noninteractive apt install -y python3-tk
+
+RUN pip install numpy
+
+# gcc-8 (cuda mex doesn't seem to work with gcc >8)
+RUN apt-get install -y gcc-8 g++-8 && ln -sf /usr/bin/gcc-8 /usr/bin/gcc && ln -sf /usr/bin/g++-8 /usr/bin/g++
+
+# Clone the source code for kilosort3
+RUN mkdir -p /src && git clone https://github.com/MouseLand/Kilosort /src/Kilosort3 && cd /src/Kilosort3 && git checkout a1fccd9abf13ce5dc3340fae8050f9b1d0f8ab7a
+
+# Note that the mex files are not actually compiled
+# I think you may need a license to do the compilation
+# Also, it may be important to compile on the machine
+# where the GPU hardware actually lives (not sure)
+
+# Also note: it is probably better to run using
+# Singularity rather than docker because
+# Singularity handles gpu more seamlessly -
+# just add the --nv flag

kilosort3/build.sh

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+#!/bin/bash
+
+# usually the tag would be the version of the sorter
+# but in this case since 3 is already in the name, maybe the tag should be 0.1.x
+docker build -t spikeinterface/kilosort3-base:0.1.0 .

kilosort3/push.sh

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+#!/bin/bash
+
+docker push spikeinterface/kilosort3-base:0.1.0