[med-svn] [salmon] 02/04: Remove salmon_core lib & unused libraires w/ patch

[Kevin Murray]

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daube-guest pushed a commit to branch kdm-cmake-dcontrol-fixes
in repository salmon.

commit 9f1fc4c0d75056f17f454e94db5a337b1f642cc4
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Sat Jan 30 18:09:48 2016 +0200

    Remove salmon_core lib & unused libraires w/ patch
---
 ...007-Remove-unnecessarily-linked-libraries.patch | 44 ++++++++++++++++++++++
 debian/patches/0008-Remove-salmon_core-lib.patch   | 42 +++++++++++++++++++++
 debian/patches/series                              |  2 +
 3 files changed, 88 insertions(+)

diff --git a/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
new file mode 100644
index 0000000..f29f1a9
--- /dev/null
+++ b/debian/patches/0007-Remove-unnecessarily-linked-libraries.patch
@@ -0,0 +1,44 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:06:06 +0200
+Subject: Remove unnecessarily linked libraries
+
+---
+ CMakeLists.txt     | 2 +-
+ src/CMakeLists.txt | 6 +-----
+ 2 files changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 378eb83..bd6393b 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -226,7 +226,7 @@ endif()
+ # Set the latest version and look for what we need
+ ##
+ set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58")
+-find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
++find_package(Boost 1.53.0 COMPONENTS filesystem system thread program_options)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 3f300c8..df31909 100755
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -112,16 +112,12 @@ target_link_libraries(salmon
+     libjellyfish-2.0.so 
+     /usr/lib/libbwa.a
+     m
+-    ${LIBLZMA_LIBRARIES}
+-    ${BZIP2_LIBRARIES}
+-    ${TBB_LIBRARIES}
++    tbb
+     ${LIBSALMON_LINKER_FLAGS}
+     ${NON_APPLECLANG_LIBS}
+     ${FAST_MALLOC_LIB}
+ )
+ 
+-add_dependencies(salmon libbwa)
+-
+ ##
+ #  This ensures that the salmon executable should work with or without `make install`
+ ##
diff --git a/debian/patches/0008-Remove-salmon_core-lib.patch b/debian/patches/0008-Remove-salmon_core-lib.patch
new file mode 100644
index 0000000..6eed4e6
--- /dev/null
+++ b/debian/patches/0008-Remove-salmon_core-lib.patch
@@ -0,0 +1,42 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 30 Jan 2016 18:06:52 +0200
+Subject: Remove salmon_core lib
+
+---
+ src/CMakeLists.txt | 8 ++------
+ 1 file changed, 2 insertions(+), 6 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index df31909..346d507 100755
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -73,11 +73,8 @@ endif()
+ 
+ set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+ 
+-# Build the Salmon library
+-add_library(salmon_core ${SALMON_LIB_SRCS} )
+-
+ # Build the salmon executable
+-add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
++add_executable(salmon ${SALMON_LIB_SRCS} ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
+ 
+ #add_executable(salmon-read ${SALMON_READ_SRCS})
+ #set_target_properties(salmon-read PROPERTIES COMPILE_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_LIBPTHREAD -D_PBGZF_USE -fopenmp"
+@@ -103,7 +100,6 @@ endif()
+ 
+ # Link the executable
+ target_link_libraries(salmon
+-    salmon_core 
+     gff
+     ${PTHREAD_LIB}
+     ${Boost_LIBRARIES} 
+@@ -158,7 +154,7 @@ endif()
+ # install(FILES ${Boost_LIBRARIES}
+ # 	           DESTINATION ${INSTALL_LIB_DIR})
+ 
+-install(TARGETS salmon salmon_core
++install(TARGETS salmon
+                 RUNTIME DESTINATION bin 
+                 LIBRARY DESTINATION lib
+                 ARCHIVE DESTINATION lib
diff --git a/debian/patches/series b/debian/patches/series
index 36557a7..02a1efc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,5 @@ drop-mathjax
 cmake-typo-fixes
 disable-version-check
 use-system-pkg-config-tbb
+0007-Remove-unnecessarily-linked-libraries.patch
+0008-Remove-salmon_core-lib.patch

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