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alejoe91alejoe91
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2 parents 2983d2f + 10f5609 commit e899860

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kilosort_no_license/README.md renamed to kilosort-compiled/README.md

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‎kilosort-compiled/compile_and_build_all_ks.sh‎

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#!/bin/bash
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set -e
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if [ $# == 0 ]; then
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echo "Usage: $0 param1 param2 param3 param4 param4"
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echo "* param1: spikeinterface path"
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echo "* param1: kilosort1 path"
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echo "* param1: kilosort2 path"
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echo "* param1: kilosort2.5 path"
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echo "* param1: kilosort3 path"
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exit
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fi
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if [ $# -ne 5 ]; then
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echo "spikeinterface and kilosort paths (1, 2, 2.5, 3) must be given"
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exit 1
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fi
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SPIKEINTERFACE_PATH=${1%/}
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KILOSORT_PATH=${2%/}
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KILOSORT2_PATH=${3%/}
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KILOSORT25_PATH=${4%/}
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KILOSORT3_PATH=${5%/}
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cd kilosort-compiled
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bash compile.sh $KILOSORT_PATH $SPIKEINTERFACE_PATH
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bash build.sh
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cd ..
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cd kilosort2-compiled
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bash compile.sh $KILOSORT2_PATH $SPIKEINTERFACE_PATH
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bash build.sh
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cd ..
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cd kilosort2_5-compiled
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bash compile.sh $KILOSORT25_PATH $SPIKEINTERFACE_PATH
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bash build.sh
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cd ..
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cd kilosort3-compiled
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bash compile.sh $KILOSORT3_PATH $SPIKEINTERFACE_PATH
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bash build.sh
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cd ..

kilosort_no_license/kilosort-compiled/Dockerfile renamed to kilosort-compiled/kilosort-compiled/Dockerfile

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FROM ks-matlab-base
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USER root
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RUN chmod 755 /usr/bin/mlrtapp/ks_compiled
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ENV PATH="/usr/bin/mlrtapp:${PATH}"
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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ENV MINICONDA_VERSION 4.8.2
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ENV MINICONDA_VERSION 23.1.0-1
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ENV PYTHON_VERSION py39
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ENV CONDA_DIR /home/miniconda3
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ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
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ENV LATEST_CONDA_SCRIPT "Miniconda3-${PYTHON_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
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RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
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bash ~/miniconda.sh -b -p $CONDA_DIR && \

kilosort_no_license/kilosort-compiled/README.md renamed to kilosort-compiled/kilosort-compiled/README.md

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kilosort_no_license/kilosort-compiled/build.sh renamed to kilosort-compiled/kilosort-compiled/build.sh

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#!/bin/bash
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docker build -t spikeinterface/kilosort-compiled-base:latest -t spikeinterface/kilosort-compiled-base:0.1.0 .
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docker build -t spikeinterface/kilosort-compiled-base:latest -t spikeinterface/kilosort-compiled-base:0.2.0 .
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kilosort_no_license/kilosort-compiled/compile.sh renamed to kilosort-compiled/kilosort-compiled/compile.sh

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echo "Compiling kilosort_master..."
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cd $TMP_DIR
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matlab -batch "mcc -m $SI_PATH/spikeinterface/sorters/kilosort/kilosort_master.m -a $SI_PATH/spikeinterface/sorters/utils -a $KS_PATH -o ${KS_COMPILED_NAME}"
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matlab -batch "mcc -m ${SI_PATH}/src/spikeinterface/sorters/external/kilosort_master.m -a ${SI_PATH}/src/spikeinterface/sorters/utils -a $KS_PATH -o ${KS_COMPILED_NAME}"
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echo "Creating base docker image..."
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matlab -batch "compiler.package.docker('${KS_COMPILED_NAME}', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')"

kilosort_no_license/kilosort-compiled/push.sh renamed to kilosort-compiled/kilosort-compiled/push.sh

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kilosort_no_license/kilosort2-compiled/Dockerfile renamed to kilosort-compiled/kilosort2-compiled/Dockerfile

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FROM ks2-matlab-base
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USER root
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RUN chmod 755 /usr/bin/mlrtapp/ks2_compiled
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ENV PATH="/usr/bin/mlrtapp:${PATH}"
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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ENV MINICONDA_VERSION 4.8.2
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ENV MINICONDA_VERSION 23.1.0-1
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ENV PYTHON_VERSION py39
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ENV CONDA_DIR /home/miniconda3
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ENV LATEST_CONDA_SCRIPT "Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh"
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ENV LATEST_CONDA_SCRIPT "Miniconda3-${PYTHON_VERSION}_${MINICONDA_VERSION}-Linux-x86_64.sh"
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RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
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bash ~/miniconda.sh -b -p $CONDA_DIR && \

kilosort_no_license/kilosort2-compiled/README.md renamed to kilosort-compiled/kilosort2-compiled/README.md

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kilosort_no_license/kilosort2-compiled/build.sh renamed to kilosort-compiled/kilosort2-compiled/build.sh

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#!/bin/bash
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docker build -t spikeinterface/kilosort2-compiled-base:latest -t spikeinterface/kilosort2-compiled-base:0.1.0 .
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docker build -t spikeinterface/kilosort2-compiled-base:latest -t spikeinterface/kilosort2-compiled-base:0.2.0 .
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