# Instructions to build patched CAPS2 on Debian/Ubuntu, tested on
# Ubuntu 20.04. Sources are provided in the current folder, but can be
# obtained from here:
wget http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.5.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-numcalc-1.8.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.7.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-1.9.0.tar.gz

wget http://bioinf.gen.tcd.ie/~faresm/software/files/caps2_src.zip

# The BppSuite components are installed in /usr/local, so they do not
# conflict with their modern versions. You _should not_ have the modern
# ones installed at CAPS2 build time, since it may get linked to them,
# instead. Build the bppSuite components in the exact order:

# Install cmake and gsl:
sudo apt install cmake

tar xvf bpp-utils-1.5.0.tar.gz
cd bpp-utils-1.5.0
sed -i "s:file;:file.good();:g" Utils/FileTools.cpp
sed -i "s:/lib/:/lib/Bpp1.9/:g" Utils.spec
mkdir -p build
cd build
cmake -DCMAKE_CXX_FLAGS:STRING="-Wl,-rpath,/usr/local/lib/Bpp1.9" -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release ..
sed -i "s:/lib\b:/lib/Bpp1.9:g" Utils/cmake_install.cmake
sed -i "s:Bpp1.9/Bpp1.9:Bpp1.9:g" Utils/cmake_install.cmake
make
sudo make install

tar xvf bpp-numcalc-1.8.0.tar.gz
cd bpp-numcalc-1.8.0
export PATH="/usr/local/lib/Bpp1.9/:$PATH"
sed -i "s:/lib/:/lib/Bpp1.9/:g" NumCalc.spec
mkdir -p build
cd build
cmake -DCMAKE_CXX_FLAGS:STRING="-Wl,-rpath,/usr/local/lib/Bpp1.9" -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release ..
sed -i "s:/lib\b:/lib/Bpp1.9:g" NumCalc/cmake_install.cmake
sed -i "s:Bpp1.9/Bpp1.9:Bpp1.9:g" NumCalc/cmake_install.cmake
make
sudo make install

tar xvf bpp-seq-1.7.0.tar.gz
cd bpp-seq-1.7.0
export PATH="/usr/local/lib/Bpp1.9/:$PATH"
sed -i "s:/lib/:/lib/Bpp1.9/:g" Seq.spec
mkdir -p build
cd build
cmake -DCMAKE_CXX_FLAGS:STRING="-Wl,-rpath,/usr/local/lib/Bpp1.9" -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release ..
sed -i "s:/lib\b:/lib/Bpp1.9:g" Seq/cmake_install.cmake
sed -i "s:Bpp1.9/Bpp1.9:Bpp1.9:g" Seq/cmake_install.cmake
make
sudo make install

tar xvf bpp-phyl-1.9.0.tar.gz
cd bpp-phyl-1.9.0
patch -p1 -i ../../caps_TreeTemplateTools.patch
export PATH="/usr/local/lib/Bpp1.9/:$PATH"
sed -i "s:/lib/:/lib/Bpp1.9/:g" Phyl.spec
mkdir -p build
cd build
cmake -DCMAKE_CXX_FLAGS:STRING="-Wl,-rpath,/usr/local/lib/Bpp1.9" -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release ..
sed -i "s:/lib\b:/lib/Bpp1.9:g" Phyl/cmake_install.cmake
sed -i "s:Bpp1.9/Bpp1.9:Bpp1.9:g" Phyl/cmake_install.cmake
make
sudo make install

# Build CAPS2:
sudo apt install libgsl-dev
cd caps2.0_src
cp Makefile.debian .
patch -p1 -i ../caps_verbose.patch
patch -p1 -i ../02_caps_sort_input.patch
make -f Makefile.debian
sudo cp vCAPS /usr/local/bin