# Minimum cmake version
cmake_minimum_required (VERSION 3.0.0)

# Name of project and that it is C++ only.
project (miniLAGAN CXX)

# ===========================================================================
# Setup Modules and Find Packages.
# ===========================================================================

set (CMAKE_MODULE_PATH "$ENV{SEQAN_ROOT}/util/cmake")
message (STATUS "CMAKE_MODULE_PATH: ${CMAKE_MODULE_PATH}")

set (SEQAN_INCLUDE_PATH "$ENV{SEQAN_ROOT}/include")
message (STATUS "SEQAN_INCLUDE_PATH: ${SEQAN_INCLUDE_PATH}")

set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)

# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------

# Update the cmake flags required for SeqAn.

set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
# Search SeqAn specific dependencies.
find_package (ZLIB)
find_package (BZip2)
find_package (SeqAn REQUIRED)

# ----------------------------------------------------------------------------
# App-Level Configuration
# ----------------------------------------------------------------------------

set (SEQAN_APP_VERSION "0.0.1")
set (SEQAN_APP_CATEGORY "Sequence Alignment")
set (CTD_PLUGIN_PACKAGE "de.demo.miniLagan")
set (CTD_PLUGIN_NAME "Demo")

set (SEQAN_VERSION_STRING "${SEQAN_APP_VERSION}")

# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------

# Add include directories.
include_directories (${SEQAN_INCLUDE_DIRS})

# Add definitions set by find_package (SeqAn).
add_definitions (${SEQAN_DEFINITIONS})

# Add definitions set by the build system.
add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
add_definitions (-DSEQAN_APP_VERSION="${SEQAN_APP_VERSION}")
add_definitions (-DSEQAN_APP_CATEGORY="${SEQAN_APP_CATEGORY}")

# Add CXX flags found by find_package (SeqAn).
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")

# Update the list of file names below if you add source files to your application.
add_executable(miniLAGAN lagan.cpp)

# Add dependencies found by find_package (SeqAn).
target_link_libraries (miniLagan ${SEQAN_LIBRARIES})

# ===========================================================================
# Setup Common Tool Description for Generic Workflow Nodes
# ===========================================================================

# Register app for CTD structure.
set (SEQAN_CTD_EXECUTABLES miniLagan CACHE INTERNAL "")
include (SeqAnCtdSetup)  # Need to be an external resource.