Add compile script - kilosort

Author: chyumin

kilosort_no_license/kilosort-compiled/compile.sh

@@ -12,26 +12,29 @@ if [ $# -ne 2 ]; then
     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: ${SI_PATH}"
+WORK_DIR=$(pwd)
+SOURCE_DIR=$( dirname -- "$0"; )
+TMP_DIR=$SOURCE_DIR/tmp
+
+echo "kilosort path: $KS_PATH"
+echo "spike-interface path: $SI_PATH"
 
 echo "Compiling CUDA files"
-cd ${KS_PATH}/CUDA
+cd $KS_PATH/CUDA
 matlab -batch "mexGPUall"
 
-cd $TMP_DIR
+echo "Creating tmp folder: $TMP_DIR"
+cd $WORK_DIR
+mkdir -p $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 "Compiling kilosort_master..."
+cd $TMP_DIR
+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
+cd $WORK_DIR
 rm -r $TMP_DIR

kilosort_no_license/kilosort2-compiled/Dockerfile

@@ -1,6 +1,6 @@
 FROM ks2-matlab-base
 
-RUN chmod 755 /usr/bin/mlrtapp/ks2_compiled
+RUN chmod 755 /usr/bin/mlrtapp/kilosort2_master
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
 RUN apt-get update -y

kilosort_no_license/kilosort2-compiled/compile.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+if [ $# == 0 ]; then
+    echo "Usage: $0 param1 param2"
+    echo "* param1: kilosort2 path"
+    echo "* param2: spikeinterface path"
+    exit
+fi
+
+if [ $# -ne 2 ]; then
+    echo "spikeinterface and kilosort2 path must be given"
+    exit 1
+fi
+
+KS_PATH=$1
+SI_PATH=$2
+WORK_DIR=$(pwd)
+SOURCE_DIR=$( dirname -- "$0"; )
+TMP_DIR=$SOURCE_DIR/tmp
+
+echo "kilosort2 path: ${KS_PATH}"
+echo "spike-interface path: ${SI_PATH}"
+
+echo "Compiling CUDA files"
+cd ${KS_PATH}/CUDA
+matlab -batch "mexGPUall"
+
+echo "Creating tmp folder: $TMP_DIR"
+cd $WORK_DIR
+mkdir -p $TMP_DIR
+
+echo "Compiling kilosort_master..."
+cd $TMP_DIR
+matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2/kilosort2_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
+
+echo "Creating base docker image..."
+matlab -batch "compiler.package.docker('kilosort2_master', 'requiredMCRProducts.txt', 'ImageName', 'ks2-matlab-base')"
+
+cd $WORK_DIR
+rm -r $TMP_DIR

kilosort_no_license/kilosort2_5-compiled/Dockerfile

@@ -1,6 +1,6 @@
 FROM ks2_5-matlab-base
 
-RUN chmod 755 /usr/bin/mlrtapp/ks2_5_compiled
+RUN chmod 755 /usr/bin/mlrtapp/kilosort2_5_master
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
 RUN apt-get update -y

kilosort_no_license/kilosort2_5-compiled/compile.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+if [ $# == 0 ]; then
+    echo "Usage: $0 param1 param2"
+    echo "* param1: kilosort2_5 path"
+    echo "* param2: spikeinterface path"
+    exit
+fi
+
+if [ $# -ne 2 ]; then
+    echo "spikeinterface and kilosort2_5 path must be given"
+    exit 1
+fi
+
+KS_PATH=$1
+SI_PATH=$2
+WORK_DIR=$(pwd)
+SOURCE_DIR=$( dirname -- "$0"; )
+TMP_DIR=$SOURCE_DIR/tmp
+
+echo "kilosort2_5 path: ${KS_PATH}"
+echo "spike-interface path: ${SI_PATH}"
+
+echo "Compiling CUDA files"
+cd ${KS_PATH}/CUDA
+matlab -batch "mexGPUall"
+
+echo "Creating tmp folder: $TMP_DIR"
+cd $WORK_DIR
+mkdir -p $TMP_DIR
+
+echo "Compiling kilosort_master..."
+cd $TMP_DIR
+matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort2_5/kilosort2_5_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
+
+echo "Creating base docker image..."
+matlab -batch "compiler.package.docker('kilosort2_5_master', 'requiredMCRProducts.txt', 'ImageName', 'ks2_5-matlab-base')"
+
+cd $WORK_DIR
+rm -r $TMP_DIR

kilosort_no_license/kilosort3-compiled/Dockerfile

@@ -1,6 +1,6 @@
 FROM ks3-matlab-base
 
-RUN chmod 755 /usr/bin/mlrtapp/ks3_compiled
+RUN chmod 755 /usr/bin/mlrtapp/kilosort3_master
 ENV PATH="/usr/bin/mlrtapp:${PATH}"
 
 RUN apt-get update -y

kilosort_no_license/kilosort3-compiled/compile.sh

@@ -0,0 +1,40 @@
+#!/bin/bash
+
+if [ $# == 0 ]; then
+    echo "Usage: $0 param1 param2"
+    echo "* param1: kilosort3 path"
+    echo "* param2: spikeinterface path"
+    exit
+fi
+
+if [ $# -ne 2 ]; then
+    echo "spikeinterface and kilosort3 path must be given"
+    exit 1
+fi
+
+KS_PATH=$1
+SI_PATH=$2
+WORK_DIR=$(pwd)
+SOURCE_DIR=$( dirname -- "$0"; )
+TMP_DIR=$SOURCE_DIR/tmp
+
+echo "kilosort3 path: ${KS_PATH}"
+echo "spike-interface path: ${SI_PATH}"
+
+echo "Compiling CUDA files"
+cd ${KS_PATH}/CUDA
+matlab -batch "mexGPUall"
+
+echo "Creating tmp folder: $TMP_DIR"
+cd $WORK_DIR
+mkdir -p $TMP_DIR
+
+echo "Compiling kilosort_master..."
+cd $TMP_DIR
+matlab -batch "mcc -m ${SI_PATH}/spikeinterface/sorters/kilosort3/kilosort3_master.m -a ${SI_PATH}/spikeinterface/sorters/utils -a ${KS_PATH}"
+
+echo "Creating base docker image..."
+matlab -batch "compiler.package.docker('kilosort3_master', 'requiredMCRProducts.txt', 'ImageName', 'ks3-matlab-base')"
+
+cd $WORK_DIR
+rm -r $TMP_DIR