#!/bin/bash
PROJECT_DIR=`pwd`
STACKS_UNTAR_DIR=${PROJECT_DIR}/stacks/untar
THIRD_PARTY_STACKS_DIR=${PROJECT_DIR}/third-party/stacks

#----------------------------------------------------------------------
# remove all last building package
#----------------------------------------------------------------------
rm -rf lib
mkdir lib
rm -rf ${STACKS_UNTAR_DIR}
rm -rf ${THIRD_PARTY_STACKS_DIR}/*
mkdir -p ${STACKS_UNTAR_DIR}
cd ${STACKS_UNTAR_DIR}
echo "End to remove all before building package ......"
#----------------------------------------------------------------------
# untar third package
#----------------------------------------------------------------------
echo "Start to untar third package ......"
for file in $(find ../tarballs -type f)
do
    tar xvf $file
done
echo "End to untar third package ......"
#----------------------------------------------------------------------
# Building jemalloc-5.2.0
#----------------------------------------------------------------------
echo "Start to build jemalloc-5.2.0 library ......"
cd jemalloc-5.2.0
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/jemalloc --with-jemalloc-prefix=je_ 
make -j4
make install
echo "End to build jemalloc-5.2.0 library ......"
#----------------------------------------------------------------------
# Building m4-1.4.18
#----------------------------------------------------------------------
echo "Start to build m4-1.4.18 library ......"
cd ../m4-1.4.18
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/m4
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/m4/bin"
echo "End to build m4-1.4.18 library ......"
#----------------------------------------------------------------------
# Building libtool-2.4.6
#----------------------------------------------------------------------
echo "Start to build libtool-2.4.6 library ......"
cd ../libtool-2.4.6
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/libtool
make
make install
echo "End to build libtool-2.4.6 library ......"
#----------------------------------------------------------------------
# Building autoconf-2.71
#----------------------------------------------------------------------
echo "Start to build autoconf-2.71 library ......"
cd ../autoconf-2.71
./configure  --prefix=${THIRD_PARTY_STACKS_DIR}/autoconf
sed -i '2211,2221 s/^/#/' Makefile
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/autoconf/bin"
echo "End to build autoconf-2.71 library ......"
#----------------------------------------------------------------------
# Building gettext-0.22.3
#----------------------------------------------------------------------
echo "Start to build gettext-0.22.3 library ......"
cd ../gettext-0.22.3
./configure  --prefix=${THIRD_PARTY_STACKS_DIR}/gettext
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/gettext/bin"
echo "End to build gettext-0.22.3 library ......"
#----------------------------------------------------------------------
# Building automake-1.16
#----------------------------------------------------------------------
echo "Start to build automake-1.16 library ......"
cd ../automake-1.16
./bootstrap
./configure  --prefix=${THIRD_PARTY_STACKS_DIR}/automake
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/automake/bin"
echo "End to build automake-1.16 library ......"
#----------------------------------------------------------------------
# Building bison-3.8
#----------------------------------------------------------------------
echo "Start to build bison-3.8 library ......"
cd ../bison-3.8
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/bison
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/bison/bin"
echo "End to build bison-3.8 library ......"
#----------------------------------------------------------------------
# Building flex-2.6.3
#----------------------------------------------------------------------
echo "Start to build flex-2.6.3 library ......"
cd ../flex-2.6.3
export LIBTOOLIZE=${THIRD_PARTY_STACKS_DIR}/libtool/bin/libtoolize
./autogen.sh
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/flex
make
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/flex/bin"
echo "End to build flex-2.6.3 library ......"
#----------------------------------------------------------------------
# Building libpcap-1.10
#----------------------------------------------------------------------
echo "Start to build libpcap-1.10 library ......"
cd ../libpcap-1.10
./autogen.sh
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/libpcap
make
make install
echo "End to build libpcap-1.10 library ......"
#----------------------------------------------------------------------
# Building openssl-3.0.1
#----------------------------------------------------------------------
echo "Start to build openssl-3.0.1 library ......"
cd ../openssl-3.0.1
./config --prefix=${THIRD_PARTY_STACKS_DIR}/openssl
make -j4
make install
cd ${THIRD_PARTY_STACKS_DIR}/openssl
ln -s lib64 lib
cd -
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${THIRD_PARTY_STACKS_DIR}/openssl/lib
echo "End to build openssl-3.0.1 library ......"
#----------------------------------------------------------------------
# Building curl-8.6.0
#----------------------------------------------------------------------
echo "Start to build curl-8.6.0 library ......"
cd ../curl-8.6.0
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/curl --with-openssl=${THIRD_PARTY_STACKS_DIR}/openssl --without-libpsl
make -j4 
make install
echo "End to build curl-8.6.0 library ......"
#----------------------------------------------------------------------
# Building boost_1_64_0
#----------------------------------------------------------------------
echo "Start to build boost_1_64_0 library ......"
BOOST_DIR=${THIRD_PARTY_STACKS_DIR}/boost_1_64_0
cd ../boost_1_64_0
./bootstrap.sh --prefix=${THIRD_PARTY_STACKS_DIR}/boost_1_64_0 --with-toolset=gcc
./b2 install toolset=gcc --with-date_time --with-regex
if  [ $? -ne 0 ];then
  echo "boost compiling failed!"
  exit
fi
echo "End to build boost_1_64_0 library ......"
#----------------------------------------------------------------------
# Building cmake-3.13.0
# del Tests Modules and # some code from CMAKELIST.txt related it 
# due to limit single file not more than 100MB on git rep
#----------------------------------------------------------------------
echo "Start to build CMake-3.26.2 library ......"
cd ../CMake-3.26.2
export OPENSSL_ROOT_DIR=${THIRD_PARTY_STACKS_DIR}/openssl
./bootstrap
make -j4 
make install DESTDIR=${THIRD_PARTY_STACKS_DIR}/cmake
ALIGNDATA_CMAKE=${THIRD_PARTY_STACKS_DIR}/cmake/usr/local/bin/./cmake
echo "End to build CMake-3.26.2 library ......"
#----------------------------------------------------------------------
# Building libubox
#----------------------------------------------------------------------
echo "Start to build libubox library ......"
cd ../libubox
${ALIGNDATA_CMAKE} -DBUILD_LUA=off -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/ubox
make install
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${THIRD_PARTY_STACKS_DIR}/ubox/include/libubox
export LIBRARY_PATH=$LIBRARY_PATH:${THIRD_PARTY_STACKS_DIR}/ubox/lib
echo "End to build libubox library ......"
#----------------------------------------------------------------------
# Building uci
#----------------------------------------------------------------------
echo "Start to build uci library ......"
cd ../uci
${ALIGNDATA_CMAKE} -DBUILD_LUA=off -DBUILD_STATIC=ON -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/uci
make install
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${THIRD_PARTY_STACKS_DIR}/uci/include
export LIBRARY_PATH=$LIBRARY_PATH:${THIRD_PARTY_STACKS_DIR}/uci/lib
echo "End to build uci library ......"
#----------------------------------------------------------------------
# Building xerces-c-3.1.4
#----------------------------------------------------------------------
echo "Start to build xerces-c-3.1.4 library ......"
cd ../xerces-c-3.1.4
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/xerces
make -j8
if  [ $? -ne 0 ];then
  echo "xerces compiling failed!"
  exit
fi
make install
echo "End to build xerces-c-3.1.4 library ......"
#----------------------------------------------------------------------
# Building ACE_wrappers
#----------------------------------------------------------------------
echo "Start to build ACE_wrappers library ......"
cd ../ACE_wrappers
export ACE_ROOT=`pwd`
cd $ACE_ROOT/ace
cp config-linux.h config.h
echo "include \$(ACE_ROOT)/include/makeinclude/platform_linux.GNU" > "${ACE_ROOT}/include/makeinclude/platform_macros.GNU"
export INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/ace
make static_libs_only=1 -j8
make install
echo "End to build ACE_wrappers library ......"
#----------------------------------------------------------------------
# Building cJSON
#----------------------------------------------------------------------
echo "Start to build cJSON library ......"
cd ${STACKS_UNTAR_DIR}/cJSON
mkdir build
cd build
${ALIGNDATA_CMAKE} .. -DBUILD_SHARED_AND_STATIC_LIBS=On -DENABLE_CJSON_TEST=Off -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/cJSON
make
make install
echo "End to build cJSON library ......"
#----------------------------------------------------------------------
# Building googletest
#----------------------------------------------------------------------
echo "Start to build googletest library ......"
cd ${STACKS_UNTAR_DIR}/googletest
mkdir build
cd build
${ALIGNDATA_CMAKE} ../ -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/googletest
make -j8
make install
echo "End to build googletest library ......"

#----------------------------------------------------------------------
# Building libevent-2.1.12-stable
#----------------------------------------------------------------------
echo "Start to build libevent library ......"
cd ${STACKS_UNTAR_DIR}/libevent-2.1.12-stable
mkdir build
cd build
${ALIGNDATA_CMAKE} ../ -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/libevent
make -j8
make install
echo "End to build libevent library ......"
#----------------------------------------------------------------------
# Building protobuf
#----------------------------------------------------------------------
echo "Start to build protobuf library ......"
cd ${STACKS_UNTAR_DIR}/protobuf
mkdir build
cd build
${ALIGNDATA_CMAKE} ../ -Dprotobuf_BUILD_SHARED_LIBS=OFF -Dprotobuf_BUILD_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/protobuf -Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_WITH_ZLIB=OFF ../ -DCMAKE_CXX_FLAGS=-fPIC -DABSL_ROOT_DIR=${STACKS_UNTAR_DIR}/abseil-cpp -DABSL_PROPAGATE_CXX_STD=ON
make -j4
make install
echo "End to build protobuf library ......"
#----------------------------------------------------------------------
# Building parquet lib
#del go Module due to limit single file no more than 100MB on git rep
#----------------------------------------------------------------------
echo "Start to build parquet library ......"
cd ${STACKS_UNTAR_DIR}/arrow/cpp
mkdir build
cd build
${ALIGNDATA_CMAKE} ../ -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/arrow -DARROW_PARQUET=ON -DARROW_OPTIONAL_INSTALL=ON -DARROW_BUILD_TESTS=ON ../
make parquet
make -j4
make install
echo "End to build parquet library ......"
#----------------------------------------------------------------------
# Building flatbuffers lib
#----------------------------------------------------------------------
echo "Start to build flatbuffers library ......"
cd ${STACKS_UNTAR_DIR}/flatbuffers
mkdir build
cd build
${ALIGNDATA_CMAKE} ../ -DCMAKE_INSTALL_PREFIX=${THIRD_PARTY_STACKS_DIR}/flatbuffers
make -j4
make install
echo "End to build flatbuffers library ......"
#----------------------------------------------------------------------
# Building texinfo-6.8 lib
#----------------------------------------------------------------------
echo "Start to build texinfo-6.8 library ......"
cd ${STACKS_UNTAR_DIR}/texinfo-6.8
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/texinfo
make -j4
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/texinfo/bin"
echo "End to build texinfo-6.8 library ......"
#----------------------------------------------------------------------
# Building help2man-1.49.3 lib
#----------------------------------------------------------------------
echo "Start to build help2man-1.49.3 library ......"
cd ${STACKS_UNTAR_DIR}/help2man-1.49.3
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/help2man
make -j4
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/help2man/bin"
echo "End to build help2man-1.49.3 library ......"
#----------------------------------------------------------------------
# Building gawk-5.3.0 lib
#----------------------------------------------------------------------
echo "Start to build gawk-5.3.0 library ......"
cd ${STACKS_UNTAR_DIR}/gawk-5.3.0
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/gawk
make -j4
make install
export PATH="$PATH:${THIRD_PARTY_STACKS_DIR}/gawk/bin"
echo "End to build gawk-5.3.0 library ......"
#----------------------------------------------------------------------
# Building gmp-6.3.0 lib
#----------------------------------------------------------------------
echo "Start to build gmp library ......"
cd ${STACKS_UNTAR_DIR}/gmp-6.3.0
./configure --prefix=${THIRD_PARTY_STACKS_DIR}/gmp
make -j4
#make check
make install
echo "End to build gmp library ......"
#----------------------------------------------------------------------
# Building litealigndata/litealigndata-package
#----------------------------------------------------------------------
echo "Start to Make package ......"
echo "Start to build litealigndata ......"
rm -rf ${PROJECT_DIR}/build
mkdir ${PROJECT_DIR}/build
cd ${PROJECT_DIR}/build
${ALIGNDATA_CMAKE}  .. -DCMAKE_INSTALL_PREFIX=${PROJECT_DIR}/litealigndata-package
make -j8

if  [ $? -ne 0 ];then
  echo "litealigndata compiling failed!"
  exit
fi
strip src/litealigndata && chmod +x src/litealigndata
make install
echo "End to build litealigndata ......"

cd ${PROJECT_DIR}
tar jcvf litealigndata-package.tar.bz2 litealigndata-package/
rm -rf litealigndata-package/

echo "End to Make package ......"