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# ===========================================================================
# SeqAn - The Library for Sequence Analysis
# ===========================================================================
# File: /apps/fx_tools/CMakeLists.txt
#
# CMakeLists.txt file for fx_tools.
# ===========================================================================
cmake_minimum_required (VERSION 3.0.0)
project (seqan_apps_fx_tools CXX)
message (STATUS "Configuring apps/fx_tools")
set (SEQAN_APP_VERSION "0.2.10")
# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------
# Search SeqAn and select dependencies.
if (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP")
find_package (SeqAn CONFIG REQUIRED)
endif ()
# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------
# Setup SeqAn requirements.
include_directories (${SEQAN_INCLUDE_DIRS})
add_definitions (${SEQAN_DEFINITIONS})
# Add definitions set by the build system.
add_definitions (-DSEQAN_APP_VERSION="${SEQAN_APP_VERSION}")
add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
# Computation of coverage and C+G content from genome and mapping.
add_executable (fx_bam_coverage fx_bam_coverage.cpp)
target_link_libraries (fx_bam_coverage ${SEQAN_LIBRARIES})
# Computation of statistics on FASTQ files.
add_executable (fx_fastq_stats fx_fastq_stats.cpp)
target_link_libraries (fx_fastq_stats ${SEQAN_LIBRARIES})
# ----------------------------------------------------------------------------
# Installation
# ----------------------------------------------------------------------------
# Set variables for installing, depending on the selected build type.
if (NOT SEQAN_PREFIX_SHARE_DOC)
seqan_setup_install_vars (fx_tools)
endif (NOT SEQAN_PREFIX_SHARE_DOC)
# Install fx_tools in ${PREFIX}/bin directory
install (TARGETS fx_bam_coverage
DESTINATION ${CMAKE_INSTALL_BINDIR})
# Install non-binary files for the package to "." for app builds and
# ${PREFIX}/share/doc/fx_tools for SeqAn release builds.
install (FILES LICENSE
README
DESTINATION ${SEQAN_PREFIX_SHARE_DOC})
#install (FILES example/fasta1.fa
# example/fasta2.fa
# DESTINATION ${SEQAN_PREFIX_SHARE_DOC}/example)
# ----------------------------------------------------------------------------
# App Test
# ----------------------------------------------------------------------------
#seqan_add_app_test (fx_tools)
# ----------------------------------------------------------------------------
# Setup Common Tool Description for Generic Workflow Nodes
# ----------------------------------------------------------------------------
# Include executable razers in CTD structure.
set (SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES} fx_fastq_stats fx_bam_coverage CACHE INTERNAL "")
# ----------------------------------------------------------------------------
# CPack Install
# ----------------------------------------------------------------------------
if (SEQAN_BUILD_SYSTEM STREQUAL "APP:fx_tools")
set (CPACK_PACKAGE_NAME "fx_tools")
set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "fx_tools")
set (CPACK_DEBIAN_PACKAGE_MAINTAINER "Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>")
set (CPACK_PACKAGE_VENDOR "Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>")
seqan_configure_cpack_app (fx_tools "fx_tools")
endif (SEQAN_BUILD_SYSTEM STREQUAL "APP:fx_tools")
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