Skip to content
Commits on Source (5)
Show whitespace changes
Inline Side-by-side
CMakeLists.txt deleted 100644 → 0
View file @ 95018739
# CMake build is not officially supported by UGENE and
# can only be used for developement (for example to enable CLion IDE integration)
#
# For CLion developers:
# * add Qt5_DIR variable to File->Settings->Build,Execution,Deployment->CMake pointing to valid QT dir.
# * add UGENE_TRANSLATION_FILE environment variable to the RUN configuration and point it to *.qm file produced by qmake build
cmake_minimum_required(VERSION 3.9)
project(ugene)
#set(CMAKE_VERBOSE_MAKEFILE ON)
set(UGENE_VERSION 1.29.0-dev)
set(UGENE_VER_MAJOR 1)
set(UGENE_VER_MINOR 29)
set(UGENE_VER_PATCH 0)
set(UGENE_MIN_VERSION_SQLITE 1.25.0)
set(UGENE_MIN_VERSION_MYSQL 1.25.0)
add_definitions(
-DUGENE_VERSION=${UGENE_VERSION}
-DUGENE_VER_MAJOR=${UGENE_VER_MAJOR}
-DUGENE_VER_MINOR=${UGENE_VER_MINOR}
-DUGENE_VER_PATCH=${UGENE_VER_PATCH}
-DUGENE_USE_BUNDLED_ZLIB
-DQT_FATAL_ASSERT
)
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -D_DEBUG")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -D_DEBUG")
# 3rd party libs
add_subdirectory(src/libs_3rdparty/breakpad)
add_subdirectory(src/libs_3rdparty/samtools)
add_subdirectory(src/libs_3rdparty/sqlite3)
add_subdirectory(src/libs_3rdparty/zlib)
# Core libs
add_subdirectory(src/corelibs/U2Core)
add_subdirectory(src/corelibs/U2Algorithm)
add_subdirectory(src/corelibs/U2Formats)
add_subdirectory(src/corelibs/U2Lang)
add_subdirectory(src/corelibs/U2Private)
add_subdirectory(src/corelibs/U2Gui)
add_subdirectory(src/corelibs/U2Test)
add_subdirectory(src/corelibs/U2Designer)
add_subdirectory(src/corelibs/U2View)
# launchers
add_subdirectory(src/ugeneui)
add_subdirectory(src/ugenecl)
# local plugins
add_subdirectory(src/plugins/annotator)
add_subdirectory(src/plugins/api_tests)
add_subdirectory(src/plugins/biostruct3d_view)
add_subdirectory(src/plugins/browser_support)
add_subdirectory(src/plugins/chroma_view)
add_subdirectory(src/plugins/circular_view)
add_subdirectory(src/plugins/CoreTests)
add_subdirectory(src/plugins/dbi_bam)
add_subdirectory(src/plugins/dna_export)
add_subdirectory(src/plugins/dna_flexibility)
add_subdirectory(src/plugins/dna_graphpack)
add_subdirectory(src/plugins/dna_stat)
add_subdirectory(src/plugins/dotplot)
add_subdirectory(src/plugins/enzymes)
add_subdirectory(src/plugins/external_tool_support)
add_subdirectory(src/plugins/genome_aligner)
# never tried: add_subdirectory(src/plugins/GUITestBase)
add_subdirectory(src/plugins/linkdata_support)
add_subdirectory(src/plugins/orf_marker)
add_subdirectory(src/plugins/pcr)
add_subdirectory(src/plugins/perf_monitor)
add_subdirectory(src/plugins/query_designer)
add_subdirectory(src/plugins/remote_blast)
add_subdirectory(src/plugins/repeat_finder)
add_subdirectory(src/plugins/smith_waterman)
add_subdirectory(src/plugins/test_runner)
add_subdirectory(src/plugins/weight_matrix)
add_subdirectory(src/plugins/workflow_designer)
# 3rd party plugins
add_subdirectory(src/plugins_3rdparty/ball)
add_subdirectory(src/plugins_3rdparty/gor4)
add_subdirectory(src/plugins_3rdparty/hmm2)
add_subdirectory(src/plugins_3rdparty/kalign)
add_subdirectory(src/plugins_3rdparty/phylip)
add_subdirectory(src/plugins_3rdparty/primer3)
add_subdirectory(src/plugins_3rdparty/psipred)
add_subdirectory(src/plugins_3rdparty/ptools)
add_subdirectory(src/plugins_3rdparty/sitecon)
add_subdirectory(src/plugins_3rdparty/umuscle)
add_subdirectory(src/plugins_3rdparty/variants)
debian/changelog
View file @ ec96824b
ugene (1.31.1+dfsg1-1) UNRELEASED; urgency=medium
* Use UGENE_USE_BUNDLED_ZLIB=1
* Use UGENE_USE_BUNDLED_ZLIB=0
* Remove psipred from upstream source - it is excluded from build anyway
* d/watch: dversionmangle=auto (to accept +dfsg[0-9])
* Add external plugins to Recommends as far as these are packaged
......
debian/copyright
View file @ ec96824b
......@@ -3,8 +3,8 @@ Upstream-Name: UGENE
Upstream-Contact: UniPro <ugene@unipro.ru>
Yuliya Algaer <yalgaer@unipro.ru>
Source: https://github.com/ugeneunipro/ugene/releases
Files-Excluded: */src/libs_3rdparty/zlib
*/src/libs_3rdparty/sqlite3
Files-Excluded: */src/libs_3rdparty/zlib/src
*/src/libs_3rdparty/sqlite3/src
*/macosx
*/windows
*/windows_x64
......@@ -20,6 +20,7 @@ Files-Excluded: */src/libs_3rdparty/zlib
src/plugins_3rdparty/psipred/src/LICENSE
src/plugins_3rdparty/psipred/datafiles
src/plugins_3rdparty/psipred/psipred.license
*/CMakeLists.txt
Files: *
Copyright: © 2008-2015 UniPro <ugene@unipro.ru>
......
debian/patches/debian_packaged_libs.patch deleted 100644 → 0
View file @ 95018739
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 31 Jan 2019 21:14:50 +0100
Description: Replace zlib and sqlite3 by Debian packaged libs
--- a/src/libs_3rdparty/samtools/src/samtools/bam.h
+++ b/src/libs_3rdparty/samtools/src/samtools/bam.h
@@ -61,7 +61,7 @@ typedef BGZF *bamFile;
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
#else
#define BAM_TRUE_OFFSET
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
typedef gzFile bamFile;
#define bam_open(fn, mode) gzopen(fn, mode)
#define bam_dopen(fd, mode) gzdopen(fd, mode)
--- a/src/libs_3rdparty/samtools/src/samtools/bam_rmdup.c
+++ b/src/libs_3rdparty/samtools/src/samtools/bam_rmdup.c
@@ -1,7 +1,7 @@
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <unistd.h>
#include "sam.h"
--- a/src/libs_3rdparty/samtools/src/samtools/bgzf.h
+++ b/src/libs_3rdparty/samtools/src/samtools/bgzf.h
@@ -26,7 +26,7 @@
#include <stdint.h>
#include <stdio.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif
--- a/src/libs_3rdparty/samtools/src/samtools/phase.c
+++ b/src/libs_3rdparty/samtools/src/samtools/phase.c
@@ -3,7 +3,7 @@
#include <unistd.h>
#include <stdint.h>
#include <math.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include "bam.h"
#include "errmod.h"
--- a/src/libs_3rdparty/samtools/src/samtools/razf.h
+++ b/src/libs_3rdparty/samtools/src/samtools/razf.h
@@ -35,7 +35,7 @@
#include <stdint.h>
#include <stdio.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#ifdef _USE_KNETFILE
#include "knetfile.h"
--- a/src/corelibs/U2Core/src/io/ZlibAdapter.cpp
+++ b/src/corelibs/U2Core/src/io/ZlibAdapter.cpp
@@ -27,7 +27,7 @@
#include "ZlibAdapter.h"
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <assert.h>
--- a/src/libs_3rdparty/samtools/src/samtools/bam_import.c
+++ b/src/libs_3rdparty/samtools/src/samtools/bam_import.c
@@ -1,4 +1,4 @@
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/bcf.h
+++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/bcf.h
@@ -31,7 +31,7 @@
#define BCF_VERSION "0.1.17-dev (r973:277)"
#include <stdint.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#ifndef BCF_LITE
#include "bgzf.h"
--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/call1.c
+++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/call1.c
@@ -1,7 +1,7 @@
#include <unistd.h>
#include <stdlib.h>
#include <math.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <errno.h>
#include "bcf.h"
#include "prob1.h"
--- a/src/libs_3rdparty/samtools/src/samtools/bcftools/vcf.c
+++ b/src/libs_3rdparty/samtools/src/samtools/bcftools/vcf.c
@@ -1,4 +1,4 @@
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
--- a/src/libs_3rdparty/samtools/src/samtools/bedidx.c
+++ b/src/libs_3rdparty/samtools/src/samtools/bedidx.c
@@ -2,7 +2,7 @@
#include <stdint.h>
#include <string.h>
#include <stdio.h>
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#ifdef _WIN32
#define drand48() ((double)rand() / RAND_MAX)
--- a/src/plugins/biostruct3d_view/src/gl2ps/gl2ps.cpp
+++ b/src/plugins/biostruct3d_view/src/gl2ps/gl2ps.cpp
@@ -72,7 +72,7 @@
#endif
#if defined(GL2PS_HAVE_ZLIB)
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#endif
#if defined(GL2PS_HAVE_LIBPNG)
--- a/src/plugins/dbi_bam/src/BAMFormat.cpp
+++ b/src/plugins/dbi_bam/src/BAMFormat.cpp
@@ -19,7 +19,7 @@
* MA 02110-1301, USA.
*/
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/L10n.h>
--- a/src/plugins/dbi_bam/src/BgzfReader.h
+++ b/src/plugins/dbi_bam/src/BgzfReader.h
@@ -22,7 +22,7 @@
#ifndef _U2_BAM_BGZF_READER_H_
#define _U2_BAM_BGZF_READER_H_
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <U2Core/IOAdapter.h>
#include "VirtualOffset.h"
--- a/src/plugins/dbi_bam/src/BgzfWriter.h
+++ b/src/plugins/dbi_bam/src/BgzfWriter.h
@@ -22,7 +22,7 @@
#ifndef _U2_BAM_BGZF_WRITER_H_
#define _U2_BAM_BGZF_WRITER_H_
-#include <3rdparty/zlib/zlib.h>
+#include <zlib.h>
#include <U2Core/IOAdapter.h>
#include "VirtualOffset.h"
debian/patches/series
View file @ ec96824b
use_debian_sqlite.patch
hardening.patch
debian_packaged_libs.patch
add_missing_header.patch
do_not_build_phylip.patch
fix_desktop_file.patch
debian/rules
View file @ ec96824b
......@@ -13,7 +13,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
override_dh_auto_configure:
# exclude non-free plugins
dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 UGENE_USE_BUNDLED_ZLIB=1
dh_auto_configure -- QMAKE_CFLAGS_ISYSTEM= QMAKE_CXXFLAGS_ISYSTEM= UGENE_WITHOUT_NON_FREE=1 UGENE_LRELEASE=lrelease-qt5 UGENE_LUPDATE=lupdate-qt5 UGENE_USE_BUNDLED_ZLIB=0
find . -name Makefile.* | xargs -r sed -i '/STRIP/d'
......
src/corelibs/U2Algorithm/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Algorithm)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOMOC ON)
find_package(Qt5 REQUIRED Core Gui Widgets)
add_definitions(-DBUILDING_U2ALGORITHM_DLL)
include_directories(src)
include_directories(../../include)
include_directories(../../libs_3rdparty/samtools/src)
include_directories(../../libs_3rdparty/samtools/src/samtools)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
qt5_add_resources(RCC_SRCS U2Algorithm.qrc)
add_library(U2Algorithm SHARED ${HDRS} ${SRCS} ${RCC_SRCS})
target_link_libraries(U2Algorithm
Qt5::Core Qt5::Gui Qt5::Widgets
samtools
U2Core)
src/corelibs/U2Core/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Core)
set(CMAKE_AUTOMOC ON)
find_package(Qt5 REQUIRED Core Gui Widgets Script Network Xml)
add_definitions(
-DBUILDING_U2CORE_DLL
-DUGENE_MIN_VERSION_SQLITE=${UGENE_MIN_VERSION_SQLITE}
-DUGENE_MIN_VERSION_MYSQL=${UGENE_MIN_VERSION_MYSQL}
)
include_directories(src)
include_directories(../../include)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
add_library(U2Core SHARED ${HDRS} ${SRCS})
target_link_libraries(U2Core
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Network Qt5::Script Qt5::Xml
ugenedb zlib)
src/corelibs/U2Designer/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Designer)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOMOC ON)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
find_package(Qt5 REQUIRED Core Gui Widgets Xml Svg Script WebKit WebKitWidgets)
add_definitions(-DBUILDING_U2DESIGNER_DLL)
include_directories(src)
include_directories(../../include)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
qt5_add_resources(RCC_SRCS U2Designer.qrc)
add_library(U2Designer SHARED ${HDRS} ${SRCS} ${RCC_SRCS})
target_link_libraries(U2Designer
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Xml Qt5::Svg Qt5::Script Qt5::WebKit Qt5::WebKitWidgets
U2Core U2Algorithm U2Gui)
src/corelibs/U2Formats/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Formats)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOMOC ON)
find_package(Qt5 REQUIRED Core Gui Widgets Sql)
add_definitions(-DBUILDING_U2FORMATS_DLL)
include_directories(src)
include_directories(../../include)
include_directories(../../libs_3rdparty/samtools/src)
include_directories(../../libs_3rdparty/samtools/src/samtools)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
qt5_add_resources(RCC_SRCS U2Formats.qrc)
add_library(U2Formats SHARED ${HDRS} ${SRCS} ${RCC_SRCS})
target_link_libraries(U2Formats
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Sql
samtools ugenedb
U2Core U2Algorithm)
src/corelibs/U2Gui/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Gui)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOMOC ON)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
find_package(Qt5 REQUIRED Core Gui Widgets Xml Network PrintSupport Svg)
add_definitions(-DBUILDING_U2GUI_DLL)
include_directories(src)
include_directories(../../include)
include_directories(../U2Private/src)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
qt5_add_resources(RCC_SRCS U2Gui.qrc)
add_library(U2Gui SHARED ${HDRS} ${SRCS} ${RCC_SRCS})
target_link_libraries(U2Gui
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Xml Qt5::Network Qt5::PrintSupport Qt5::Svg
U2Core U2Algorithm U2Formats U2Private)
src/corelibs/U2Lang/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Lang)
set(CMAKE_AUTORCC ON)
set(CMAKE_AUTOMOC ON)
find_package(Qt5 REQUIRED Core Xml Script)
add_definitions(-DBUILDING_U2LANG_DLL)
include_directories(src)
include_directories(../../include)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
qt5_add_resources(RCC_SRCS U2Lang.qrc)
add_library(U2Lang SHARED ${HDRS} ${SRCS} ${RCC_SRCS})
target_link_libraries(U2Lang
Qt5::Core Qt5::Xml Qt5::Script
U2Core)
src/corelibs/U2Private/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Private)
set(CMAKE_AUTOMOC ON)
if (APPLE)
find_package(Qt5 REQUIRED Core Gui Widgets Xml)
else()
find_package(Qt5 REQUIRED Core Gui Widgets)
endif()
add_definitions(-DBUILDING_U2PRIVATE_DLL)
include_directories(src)
include_directories(../../include)
include_directories(../../libs_3rdparty/breakpad/src)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
file(GLOB_RECURSE WIN_IGNORE_FILES src/*Mac.* src/*UnixNotMac.*)
file(GLOB_RECURSE MAC_IGNORE_FILES src/*Win.* src/*UnixNotMac.*)
file(GLOB_RECURSE LINUX_IGNORE_FILES src/*[er]Mac.* src/*Win.*)
if (WIN32)
list(REMOVE_ITEM SRCS ${WIN_IGNORE_FILES})
list(REMOVE_ITEM HDRS ${WIN_IGNORE_FILES})
elseif (APPLE)
list(REMOVE_ITEM SRCS ${MAC_IGNORE_FILES})
list(REMOVE_ITEM HDRS ${MAC_IGNORE_FILES})
elseif (UNIX)
list(REMOVE_ITEM SRCS ${LINUX_IGNORE_FILES})
list(REMOVE_ITEM HDRS ${LINUX_IGNORE_FILES})
endif ()
add_library(U2Private SHARED ${HDRS} ${SRCS})
target_link_libraries(U2Private
Qt5::Core Qt5::Gui Qt5::Widgets
breakpad
U2Core U2Algorithm U2Formats)
if (APPLE)
target_link_libraries(U2Private Qt5::Xml "-framework CoreFoundation -framework IOKit")
endif()
src/corelibs/U2Test/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2Test)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTOMOC ON)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
find_package(Qt5 REQUIRED Core Gui Widgets Xml)
add_definitions(-DBUILDING_U2TEST_DLL)
include_directories(src)
include_directories(../../include)
file(GLOB SRCS src/*.cpp src/xmltest/*.cpp)
file(GLOB HDRS src/*.h src/xmltest/*.h)
add_library(U2Test SHARED ${HDRS} ${SRCS})
target_link_libraries(U2Test
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Xml
U2Core)
src/corelibs/U2View/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(U2View)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTOMOC ON)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
find_package(Qt5 REQUIRED Core Gui Widgets Xml Svg WebKit WebKitWidgets PrintSupport)
add_definitions(-DBUILDING_U2VIEW_DLL)
include_directories(src)
include_directories(../../include)
file(GLOB_RECURSE SRCS src/*.cpp)
file(GLOB_RECURSE HDRS src/*.h)
add_library(U2View SHARED ${HDRS} ${SRCS})
target_link_libraries(U2View
Qt5::Core Qt5::Gui Qt5::Widgets Qt5::Xml Qt5::Svg Qt5::WebKit Qt5::WebKitWidgets Qt5::PrintSupport
U2Core U2Algorithm U2Formats U2Lang U2Gui)
src/libs_3rdparty/breakpad/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(breakpad)
include_directories(src)
file(GLOB COMMON_SRCS src/client/*.cc src/common/*.cc src/common/*.c)
file(GLOB COMMON_HDRS src/client/*.h src/common/*.h)
if (WIN32)
file(GLOB_RECURSE SRCS src/client/windows/*.cc src/common/windows/*.cc)
file(GLOB_RECURSE HDRS src/client/windows/*.h src/common/windows/*.h)
elseif (APPLE)
file(GLOB_RECURSE SRCS src/client/mac/*.cc src/common/mac/*.cc src/common/mac/*.mm)
file(GLOB_RECURSE HDRS src/client/mac/*.h src/common/mac/*.h)
elseif (UNIX)
file(GLOB_RECURSE SRCS src/client/linux/*.cc src/common/linux/*.cc)
file(GLOB_RECURSE HDRS src/client/linux/*.h src/common/linux/*.h)
endif ()
add_library(breakpad SHARED ${COMMON_HDRS} ${HDRS} ${COMMON_SRCS} ${SRCS})
target_link_libraries(breakpad)
if (APPLE)
target_link_libraries(breakpad "-framework CoreFoundation")
target_link_libraries(breakpad "-framework Security")
endif ()
src/libs_3rdparty/samtools/CMakeLists.txt deleted 100644 → 0
View file @ 95018739
cmake_minimum_required(VERSION 3.4)
project(samtools)
set(CMAKE_AUTOMOC ON)
find_package(Qt5 REQUIRED Core LinguistTools)
include_directories(src)
include_directories(src/samtools)
include_directories(../../include)
add_definitions(
-D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE
-D_USE_KNETFILE
)
file(GLOB_RECURSE SRCS src/*.cpp src/*.c)
file(GLOB_RECURSE HDRS src/*.h)
file(GLOB TS_FILES transl/*.ts)
qt5_add_translation(QM_FILES ${TS_FILES})
# Supress original samtools warnings
if (CMAKE_COMPILER_IS_GNUCC)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w")
endif (CMAKE_COMPILER_IS_GNUCC)
add_library(samtools STATIC ${HDRS} ${SRCS} ${QM_FILES})
target_link_libraries(samtools
Qt5::Core
zlib)
src/libs_3rdparty/sqlite3/sqlite3.pri 0 → 100644
View file @ ec96824b
# include (sqlite.pri)
include( ../../ugene_globals.pri )
UGENE_RELATIVE_DESTDIR = ''
TARGET = ugenedb
TEMPLATE = lib
CONFIG +=thread debug_and_release warn_off
INCLUDEPATH += src
DEFINES+=SQLITE_ENABLE_COLUMN_METADATA
DEFINES+=SQLITE_ENABLE_RTREE
unix:DEFINES+=SQLITE_OMIT_LOAD_EXTENSION
DEFINES+=THREADSAFE
LIBS += -L../../_release
!debug_and_release|build_pass {
CONFIG(debug, debug|release) {
TARGET = ugenedbd
DEFINES+=_DEBUG
CONFIG +=console
DESTDIR=../../_debug/
OBJECTS_DIR=_tmp/obj/debug
LIBS -= -L../../_release
LIBS += -L../../_debug
}
CONFIG(release, debug|release) {
TARGET = ugenedb
DEFINES+=NDEBUG
DESTDIR=../../_release/
OBJECTS_DIR=_tmp/obj/release
}
}
win32 {
DEF_FILE=$$PWD/src/sqlite3.def
QMAKE_CXXFLAGS_WARN_ON = -W3
QMAKE_CFLAGS_WARN_ON = -W3
QMAKE_MSVC_PROJECT_NAME=lib_3rd_sqlite3
}
unix {
target.path = $$UGENE_INSTALL_DIR/$$UGENE_RELATIVE_DESTDIR
INSTALLS += target
}
macx {
QMAKE_RPATHDIR += @executable_path/
QMAKE_LFLAGS_SONAME = -Wl,-dylib_install_name,@rpath/
}
src/libs_3rdparty/sqlite3/sqlite3.pro 0 → 100644
View file @ ec96824b
include (sqlite3.pri)
# Input
HEADERS += src/sqlite3.h
SOURCES += src/sqlite3.c
\ No newline at end of file
src/libs_3rdparty/zlib/zlib.pri 0 → 100644
View file @ ec96824b
include( ../../ugene_globals.pri )
UGENE_RELATIVE_DESTDIR = ''
TEMPLATE = lib
CONFIG +=thread debug_and_release staticlib
DEFINES+= _CRT_SECURE_NO_WARNINGS
INCLUDEPATH += src
TARGET = zlib
DESTDIR=../../_release
!debug_and_release|build_pass {
CONFIG(debug, debug|release) {
TARGET = zlibd
DEFINES+=_DEBUG
CONFIG +=console
DESTDIR=../../_debug
OBJECTS_DIR=_tmp/obj/debug
MOC_DIR=_tmp/moc/debug
}
CONFIG(release, debug|release) {
DEFINES+=NDEBUG
OBJECTS_DIR=_tmp/obj/release
MOC_DIR=_tmp/moc/release
}
}
UI_DIR=_tmp/ui
RCC_DIR=_tmp/rcc
win32 {
QMAKE_CXXFLAGS_WARN_ON = -W3
QMAKE_CFLAGS_WARN_ON = -W3
QMAKE_CXXFLAGS+=/wd4996
QMAKE_MSVC_PROJECT_NAME=lib_3rd_zlib
}
macx {
QMAKE_RPATHDIR += @executable_path/
QMAKE_LFLAGS_SONAME = -Wl,-dylib_install_name,@rpath/
}
#unix {
# target.path = $$UGENE_INSTALL_DIR/$$UGENE_RELATIVE_DESTDIR
# INSTALLS += target
#}