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debian/patches/correct_cflags.patch → debian/patches/0001-correct_cflags.patch
View file @ 2ec383ce
Author: Gert Wollny <gw.fossdev@gmail.com>
Last-Update: Mon, 22 Jun 2015 15:49:39 +0200
Description: Fix cmake file
The htqc authors might have used a version of cmake that interprets the
CMAKE_CXX_FLAGS as a list, and Elements of lists in cmake are separated
by ';'.
.
Apparently this is no longer possible so you'll have to (re-)set the
cxx_flags string directly.
From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Date: Tue, 23 Jun 2015 13:16:51 +0200
Subject: correct_cflags
---
CMakeLists.txt | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 73d0f1a..90fadcb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,7 +22,7 @@ if (CMAKE_BUILD_TYPE STREQUAL "")
......
debian/patches/0002-Added-Debian-specific-SONAMEs.patch.patch 0 → 100644
View file @ 2ec383ce
From: Leopold Palomo-Avellaneda <leopold.palomo@upc.edu>
Date: Tue, 23 Jun 2015 15:23:35 +0200
Subject: Added Debian specific SONAMEs.patch
---
src/CMakeLists.txt | 80 ++++++++++++++++++++++++++++++++++++++----------------
t/CMakeLists.txt | 66 ++++++++++++++++++++++----------------------
2 files changed, 90 insertions(+), 56 deletions(-)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a3bb0fc..6e0cf3c 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -5,22 +5,54 @@ file(GLOB HTIO_SOURCE_FILES htio2/*.cpp)
file(GLOB HTQC_SOURCE_FILES htqc/*.cpp)
file(GLOB JUCE_SOURCE_FILES htio2/JUCE-3.0.8/modules/*/*.cpp)
-add_library(htio2 STATIC ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
+add_library(htio2_static STATIC ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
+set_target_properties(htio2_static PROPERTIES
+ OUTPUT_NAME htio2
+ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
+ CLEAN_DIRECT_OUTPUT 1)
-add_library(ht_common STATIC ${HTQC_SOURCE_FILES})
+#CPACK_PACKAGE_VERSION_MAJOR 1
+#CPACK_PACKAGE_VERSION_MINOR 92
+#CPACK_PACKAGE_VERSION_PATCH 1
+
+add_library(htio2_dynamic SHARED ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
+set_target_properties( htio2_dynamic PROPERTIES
+ VERSION
+"${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}"
+ SOVERSION ${CPACK_PACKAGE_VERSION_MAJOR}
+ OUTPUT_NAME htio2
+ LINK_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}"
+ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
+ CLEAN_DIRECT_OUTPUT 1)
+
+add_library(ht_common_static STATIC ${HTQC_SOURCE_FILES})
+set_target_properties(ht_common_static PROPERTIES
+ OUTPUT_NAME ht_common
+ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
+ CLEAN_DIRECT_OUTPUT 1)
+
+add_library(ht_common_dynamic SHARED ${HTQC_SOURCE_FILES})
+set_target_properties( ht_common_dynamic PROPERTIES
+ VERSION
+"${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}"
+ SOVERSION "${CPACK_PACKAGE_VERSION_MAJOR}"
+ OUTPUT_NAME ht_common
+ LINK_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}"
+ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
+ CLEAN_DIRECT_OUTPUT 1)
add_executable(ht2-convert ht2-convert.cpp)
target_link_libraries(ht2-convert
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-demul ht2-demul.cpp)
target_link_libraries(ht2-demul
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -30,71 +62,73 @@ add_executable(ht2-stat ht2-stat.cpp
htqc/FastqStat.cpp
)
target_link_libraries(ht2-stat
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-trim ht2-trim.cpp)
target_link_libraries(ht2-trim
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-filter ht2-filter.cpp)
target_link_libraries(ht2-filter
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-rename ht2-rename.cpp)
target_link_libraries(ht2-rename
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-sample ht2-sample.cpp)
target_link_libraries(ht2-sample
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-overlap ht2-overlap.cpp)
target_link_libraries(ht2-overlap
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-primer-trim ht2-primer-trim.cpp)
target_link_libraries(ht2-primer-trim
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
add_executable(ht2-lane-tile ht2-lane-tile.cpp)
target_link_libraries(ht2-lane-tile
- ht_common
- htio2
+ ht_common_dynamic
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
-install(TARGETS ht2-demul ht2-primer-trim ht2-convert ht2-stat ht2-trim ht2-filter ht2-sample ht2-overlap ht2-rename htio2
+install(TARGETS ht2-demul ht2-primer-trim ht2-convert ht2-stat ht2-trim ht2-filter ht2-sample ht2-overlap ht2-rename htio2_dynamic
+ htio2_static ht_common_static ht_common_dynamic
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
)
install(PROGRAMS ht2-stat-draw.pl DESTINATION bin)
install(FILES ${CMAKE_BINARY_DIR}/src/htio2/config.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/htio2)
diff --git a/t/CMakeLists.txt b/t/CMakeLists.txt
index 6ca515a..e44b87f 100644
--- a/t/CMakeLists.txt
+++ b/t/CMakeLists.txt
@@ -1,12 +1,12 @@
include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
configure_file(TestConfig.h.in TestConfig.h ESCAPE_QUOTES)
-add_library(TestFramework TestFramework.cpp)
+add_library(TestFramework SHARED TestFramework.cpp)
add_executable(t_text_file_equal t_text_file_equal.cpp)
target_link_libraries(t_text_file_equal
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -15,7 +15,7 @@ add_test(text_file_equal t_text_file_equal)
add_executable(t_kmer_nt5_16 t_kmer_nt5_16.cpp)
target_link_libraries(t_kmer_nt5_16
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -24,7 +24,7 @@ add_test(kmer_nt5_16 t_kmer_nt5_16)
add_executable(t_kmer_nt5_32 t_kmer_nt5_32.cpp)
target_link_libraries(t_kmer_nt5_32
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -33,7 +33,7 @@ add_test(kmer_nt5_32 t_kmer_nt5_32)
add_executable(t_kmer_nt5_64 t_kmer_nt5_64.cpp)
target_link_libraries(t_kmer_nt5_64
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -42,7 +42,7 @@ add_test(kmer_nt5_64 t_kmer_nt5_64)
add_executable(t_kmer_nt4_16 t_kmer_nt4_16.cpp)
target_link_libraries(t_kmer_nt4_16
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -51,7 +51,7 @@ add_test(kmer_nt4_16 t_kmer_nt4_16)
add_executable(t_kmer_nt4_32 t_kmer_nt4_32.cpp)
target_link_libraries(t_kmer_nt4_32
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -60,7 +60,7 @@ add_test(kmer_nt4_32 t_kmer_nt4_32)
add_executable(t_kmer_nt4_64 t_kmer_nt4_64.cpp)
target_link_libraries(t_kmer_nt4_64
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -69,7 +69,7 @@ add_test(kmer_nt4_64 t_kmer_nt4_64)
add_executable(t_kmer_aa t_kmer_aa.cpp)
target_link_libraries(t_kmer_aa
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -78,7 +78,7 @@ add_test(kmer_aa t_kmer_aa)
add_executable(t_ref_counted t_ref_counted.cpp)
target_link_libraries(t_ref_counted
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -87,7 +87,7 @@ add_test(ref_counted t_ref_counted)
add_executable(t_simple_seq t_simple_seq.cpp)
target_link_libraries(t_simple_seq
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -96,7 +96,7 @@ add_test(simple_seq t_simple_seq)
add_executable(t_plain_file_handle t_plain_file_handle.cpp)
target_link_libraries(t_plain_file_handle
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -105,7 +105,7 @@ add_test(plain_file_handle t_plain_file_handle)
add_executable(t_gzip_file_handle t_gzip_file_handle.cpp)
target_link_libraries(t_gzip_file_handle
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -114,7 +114,7 @@ add_test(gzip_file_handle t_gzip_file_handle)
add_executable(t_fastq_io t_fastq_io.cpp)
target_link_libraries(t_fastq_io
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -123,7 +123,7 @@ add_test(fastq_io t_fastq_io)
add_executable(t_fasta_io t_fasta_io.cpp)
target_link_libraries(t_fasta_io
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -132,7 +132,7 @@ add_test(fasta_io t_fasta_io)
add_executable(t_header_util t_header_util.cpp)
target_link_libraries(t_header_util
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -141,8 +141,8 @@ add_test(header_util t_header_util)
add_executable(t_multi_seq_file_se t_multi_seq_file_se.cpp)
target_link_libraries(t_multi_seq_file_se
TestFramework
- ht_common
- htio2
+ htio2_dynamic
+ ht_common_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -151,8 +151,8 @@ add_test(multi_seq_file_se t_multi_seq_file_se)
add_executable(t_multi_seq_file_pe t_multi_seq_file_pe.cpp)
target_link_libraries(t_multi_seq_file_pe
TestFramework
- ht_common
- htio2
+ htio2_dynamic
+ ht_common_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -161,7 +161,7 @@ add_test(multi_seq_file_pe t_multi_seq_file_pe)
add_executable(t_ht_sample t_ht_sample.cpp)
target_link_libraries(t_ht_sample
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -170,7 +170,7 @@ add_test(ht_sample t_ht_sample)
add_executable(t_ht_trim t_ht_trim.cpp)
target_link_libraries(t_ht_trim
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -179,7 +179,7 @@ add_test(ht_trim t_ht_trim)
add_executable(t_ht_rename t_ht_rename.cpp)
target_link_libraries(t_ht_rename
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -188,7 +188,7 @@ add_test(ht_rename t_ht_rename)
add_executable(t_ht_overlap t_ht_overlap.cpp)
target_link_libraries(t_ht_overlap
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -197,7 +197,7 @@ add_test(ht_overlap t_ht_overlap)
add_executable(t_ht_filter t_ht_filter.cpp)
target_link_libraries(t_ht_filter
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -206,7 +206,7 @@ add_test(ht_filter t_ht_filter)
add_executable(t_ht_convert t_ht_convert.cpp)
target_link_libraries(t_ht_convert
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -215,7 +215,7 @@ add_test(ht_convert t_ht_convert)
add_executable(t_ht_demul t_ht_demul.cpp)
target_link_libraries(t_ht_demul
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -224,7 +224,7 @@ add_test(ht_demul t_ht_demul)
add_executable(t_ht_lane_tile t_ht_lane_tile.cpp)
target_link_libraries(t_ht_lane_tile
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -233,7 +233,7 @@ add_test(ht_lane_tile t_ht_lane_tile)
add_executable(t_string t_string.cpp)
target_link_libraries(t_string
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -242,7 +242,7 @@ add_test(string t_string)
add_executable(t_cast t_cast.cpp)
target_link_libraries(t_cast
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -250,7 +250,7 @@ add_test(cast t_cast)
add_executable(option_parser option_parser.cpp)
target_link_libraries(option_parser
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -258,7 +258,7 @@ target_link_libraries(option_parser
add_executable(t_ring_buffer t_ring_buffer.cpp)
target_link_libraries(t_ring_buffer
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
@@ -267,7 +267,7 @@ add_test(ring_buffer t_ring_buffer)
add_executable(t_mt19937 t_mt19937.cpp)
target_link_libraries(t_mt19937
TestFramework
- htio2
+ htio2_dynamic
${juce_dep_libs}
${ZLIB_LIBRARIES}
)
debian/patches/enable_testing.patch → debian/patches/0003-enable_testing.patch
View file @ 2ec383ce
Author: Leopold Palomo-Avellaneda <leo@alaxarxa.net>
Last-Update: Tue, 23 Jun 2015 09:51:43 +0200
Description: Enable testing
From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Date: Tue, 23 Jun 2015 15:29:55 +0200
Subject: enable_testing
---
CMakeLists.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 90fadcb..716aad5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,5 +53,6 @@ include_directories(
......
debian/patches/series
View file @ 2ec383ce
correct_cflags.patch
enable_testing.patch
0001-correct_cflags.patch
0002-Added-Debian-specific-SONAMEs.patch.patch
0003-enable_testing.patch