New upstream version 2.3.0

/build

[submodule "thirdparty/gatb-core"]

	path = thirdparty/gatb-core

	url = https://github.com/GATB/gatb-core.git

project(DiscoSNP++)

cmake_minimum_required(VERSION 2.6)

################################################################################

# The version number.

################################################################################

SET (gatb-tool_VERSION_MAJOR 2)

SET (gatb-tool_VERSION_MINOR 2)

SET (gatb-tool_VERSION_PATCH 10)

IF (DEFINED MAJOR)

    SET (gatb-tool_VERSION_MAJOR ${MAJOR})

ENDIF()

IF (DEFINED MINOR)

    SET (gatb-tool_VERSION_MINOR ${MINOR})

ENDIF()

IF (DEFINED PATCH)

    SET (gatb-tool_VERSION_PATCH ${PATCH})

ENDIF()

set (gatb-tool-version ${gatb-tool_VERSION_MAJOR}.${gatb-tool_VERSION_MINOR}.${gatb-tool_VERSION_PATCH})

# However, continuous integration has priority over local compilation

IF (DEFINED JENKINS_TAG)

    SET (gatb-tool-version ${JENKINS_TAG})

ENDIF()

################################################################################

# Define cmake modules directory

################################################################################

SET (GATB_CORE_HOME  ${PROJECT_SOURCE_DIR}/thirdparty/gatb-core/gatb-core)

SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake)

################################################################################

# THIRD PARTIES

################################################################################

# We don't want to install some GATB-CORE artifacts

SET (GATB_CORE_EXCLUDE_TESTS     1)

SET (GATB_CORE_EXCLUDE_EXAMPLES  1)

# GATB CORE

include (GatbCore)

################################################################################

#  TOOLS GENERATION

################################################################################

SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)

set(PROJECT_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/bin)

#set(PROJECT_BINARY_DIR bin)

ADD_SUBDIRECTORY(tools)

################################################################################

#  PACKAGING

################################################################################

SET (CPACK_PACKAGE_DESCRIPTION_SUMMARY  "gatb-tool ${PROJECT_NAME}")

SET (CPACK_PACKAGE_VENDOR               "Genscale team (INRIA)")

SET (CPACK_PACKAGE_VERSION_MAJOR        "${gatb-tool_VERSION_MAJOR}")

SET (CPACK_PACKAGE_VERSION_MINOR        "${gatb-tool_VERSION_MINOR}")

SET (CPACK_PACKAGE_VERSION_PATCH        "${gatb-tool_VERSION_PATCH}")

SET (CPACK_PACKAGE_VERSION              "${gatb-tool-version}")

# We chose the kind of archive we want to generate

SET (CPACK_GENERATOR            "TGZ")

SET (CPACK_SOURCE_GENERATOR     "TGZ")

# We ignore unwanted files for the source archive

SET (CPACK_SOURCE_IGNORE_FILES

    "^${PROJECT_SOURCE_DIR}/\\.git/"     ;

    "^${PROJECT_SOURCE_DIR}/\\.gitmodules" ;

    "^${PROJECT_SOURCE_DIR}/\\.gitignore" ;

    "^${PROJECT_SOURCE_DIR}/build/"  ;

    "^${GATB_CORE_HOME}/\\.cproject" ;

    "^${GATB_CORE_HOME}/\\.git/"     ;

    "^${GATB_CORE_HOME}/\\.project"  ;

    "^${GATB_CORE_HOME}/\\.gitignore"

)

# For creating the BINARY package we include the files we want

INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc                DESTINATION .)

INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/test               DESTINATION .)

INSTALL (DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/scripts            DESTINATION . FILES_MATCHING REGEX ".*\\.(py|sh)$"  PATTERN "jenkins" EXCLUDE)

INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/run_discoSnp++.sh  DESTINATION .)

INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/README.md          DESTINATION .)

INSTALL (FILES     ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE            DESTINATION .)

# We include the "bin" tag into binary archive file name

set (CPACK_PACKAGE_FILE_NAME  ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})

# To be done at the end.

INCLUDE (CPack)

# CMake is required to compile software (http://www.cmake.org/cmake/resources/software.html)

#

# You can install software by executing this file: sh INSTALL

#

# Prepare GATB sub-module

git submodule init

git submodule update

# Prepare directories:

rm -rf build

mkdir  build

# Go in the 'build' directory

cd build

# Prepare the makefile

cmake ..

# Run the newly created makefile:

make -j8

# Go back at the installation root directory

cd ..

# run tests

echo "Running simple test..."

cd test

. ./simple_test.sh

cd ..