setup-biorobotics-dev-environment.sh

#!/bin/sh

CURRENT_DIR=`pwd`
ROOT_DIR=$CURRENT_DIR/biorobotics-dev-environment
SRC_DIR=$ROOT_DIR/source
NUM_CORES=`nproc`
NUM_THREADS=$(($NUM_CORES + 1))

if [ -d "$ROOT_DIR" ]; then
        echo 'Folder already exists.'
exit
fi

mkdir -p $SRC_DIR

git clone [email protected]:BioroboticsLab/biotracker_core.git $SRC_DIR/biotracker_core
git clone [email protected]:BioroboticsLab/biotracker_gui.git $SRC_DIR/biotracker_gui
git clone [email protected]:BioroboticsLab/deeplocalizer_classifier.git $SRC_DIR/deeplocalizer_classifier
git clone [email protected]:BioroboticsLab/pipeline.git $SRC_DIR/pipeline
git clone [email protected]:BioroboticsLab/deeplocalizer_tagger.git $SRC_DIR/deeplocalizer_tagger
git clone [email protected]:BioroboticsLab/parameteroptimization.git $SRC_DIR/parameteroptimization

cd $SRC_DIR/deeplocalizer_classifier
git checkout cpm

cd $SRC_DIR/pipeline
git checkout cpm

for BUILD_TYPE in Debug RelWithDebInfo Release; do
        BUILD_DIR=$ROOT_DIR/build/$BUILD_TYPE

        mkdir -p $BUILD_DIR

        mkdir -p $BUILD_DIR/biotracker_core
        cd $BUILD_DIR/biotracker_core
        cmake -Wno-dev -DCMAKE_BUILD_TYPE=$BUILD_TYPE $SRC_DIR/biotracker_core
        make -j $NUM_THREADS

        mkdir -p $BUILD_DIR/biotracker_gui
        cd $BUILD_DIR/biotracker_gui
        cmake -Wno-dev -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBIOTRACKER_CORE_PATH=$SRC_DIR/biotracker_core $SRC_DIR/biotracker_gui
        make -j $NUM_THREADS

        mkdir -p $BUILD_DIR/deeplocalizer_classifier
        cd $BUILD_DIR/deeplocalizer_classifier
        cmake -Wno-dev -DCMAKE_BUILD_TYPE=$BUILD_TYPE $SRC_DIR/deeplocalizer_classifier
        make -j $NUM_THREADS

        mkdir -p $BUILD_DIR/pipeline
        cd $BUILD_DIR/pipeline
        cmake -Wno-dev -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DDEEPLOCALIZER_CLASSIFIER_PATH=$SRC_DIR/deeplocalizer_classifier $SRC_DIR/pipeline
        make -j $NUM_THREADS

        mkdir -p $BUILD_DIR/parameteroptimization
        cd $BUILD_DIR/parameteroptimization
        cmake -Wno-dev -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBIOTRACKER_CORE_PATH=$SRC_DIR/biotracker_core -DPIPELINE_PATH=$SRC_DIR/pipeline -DDEEPLOCALIZER_CLASSIFIER_PATH=$SRC_DIR/deeplocalizer_classifier $SRC_DIR/parameteroptimization
        make -j $NUM_THREADS
done