Using spikeinterface's matlab files. compile script v1

Author: chyumin

kilosort_no_license/kilosort-compiled/Dockerfile

@@ -1,6 +1,6 @@
 FROM ks-matlab-base
 
-RUN chmod 755 /usr/bin/mlrtapp/ks_compiled
+RUN chmod 755 /usr/bin/mlrtapp/kilosort_master
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
 RUN apt-get update -y
@@ -13,4 +13,3 @@ RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10
 RUN apt-get install python3-pip -y
 RUN update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
 RUN pip install -U pip
-

kilosort_no_license/kilosort-compiled/README.md

@@ -1,6 +1,6 @@
 # Generating Compiled Kilosort Docker Image
 
-## 1. Kilosort Setup 
+## 1. Kilosort Setup
 - Git clone or Download Kilosort [source code](https://github.com/cortex-lab/KiloSort)
 - Open Matlab
 - Compile Kilosort mexfiles:

kilosort_no_license/kilosort-compiled/compile.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+if [ $# == 0 ]; then
+    echo "Usage: $0 param1 param2"
+    echo "* param1: KiloSort path"
+    echo "* param2: spikeinterface path"
+    exit
+fi
+
+if [ $# -ne 2 ]; then
+    echo "spikeinterface and kilosort path must be given"
+    exit 1
+fi
+
+ROOT_PATH=$(pwd)
+echo "Creating tmp folder in: ${ROOT_PATH}"
+mkdir -p tmp
+TMP_DIR=$ROOT_PATH/tmp
+KS_PATH=$1
+SI_PATH=$2
+echo "Kilosort path: ${KS_PATH}"
+echo "spike-interface path: ${SI_PATH}"
+
+echo "Compiling CUDA files"
+cd ${KS_PATH}/CUDA
+matlab -batch "mexGPUall"
+
+cd $TMP_DIR
+
+echo "Compiling kilosort_master from spikeinterface repository..."
+matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort/kilosort_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
+
+echo "Creating base docker image..."
+matlab -batch "compiler.package.docker('kilosort_master', 'requiredMCRProducts.txt', 'ImageName', 'ks-matlab-base')"
+
+cd $ROOT_PATH
+rm -r $TMP_DIR