Take over patches from previous version if applicable. Keep some for documentation purpose

From: Kevin Murray <spam@kdmurray.id.au>

Date: Sat, 30 Jan 2016 18:06:52 +0200

Subject: Remove salmon_core lib

Remark: This patch is deactivated

 Upstream code has changed a lot and it is not documented why

 salmon_core lib was removed.  Before breaking anything the

 hopefully harmles lib is created as upstream seems to consider

 sensible.

---

 src/CMakeLists.txt | 8 ++------

 1 file changed, 2 insertions(+), 6 deletions(-)

--- a/src/CMakeLists.txt

+++ b/src/CMakeLists.txt

@@ -102,9 +102,6 @@

   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)

 endif()

-# Build the Salmon library

-add_library(salmon_core ${SALMON_LIB_SRCS} )

-

 # Build the salmon executable

 add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})

@@ -124,7 +121,6 @@

 # Link the executable

 target_link_libraries(salmon

-    salmon_core

     gff

     ${PTHREAD_LIB}

     ${Boost_LIBRARIES}

@@ -146,42 +142,41 @@

 # External dependencies of salmon_core and salmon

 ##

 if (${FETCHED_JEMALLOC})

-   add_dependencies(salmon_core libjemalloc)

+    #   add_dependencies(salmon_core libjemalloc)

    add_dependencies(salmon libjemalloc)

 endif()

 if (${FETCHED_BOOST})

-   add_dependencies(salmon_core libboost)

+    # add_dependencies(salmon_core libboost)

    add_dependencies(salmon libboost)

 endif()

 if (${FETCHED_JELLYFISH})

-   add_dependencies(salmon_core libjellyfish)

+    #add_dependencies(salmon_core libjellyfish)

    add_dependencies(salmon libjellyfish)

 endif()

 if (${FETCHED_TBB})

-   add_dependencies(salmon_core libtbb)

+    #add_dependencies(salmon_core libtbb)

    add_dependencies(salmon libtbb)

 endif()

-add_dependencies(salmon_core libcereal)

+#add_dependencies(salmon_core libcereal)

 add_dependencies(salmon libcereal)

-add_dependencies(salmon_core libstadenio)

+#add_dependencies(salmon_core libstadenio)

 add_dependencies(salmon libstadenio)

-add_dependencies(salmon_core libspdlog)

+#add_dependencies(salmon_core libspdlog)

 add_dependencies(salmon libspdlog)

 ## FIXME: This was commented in version 0.7.2 in a quilt patch

-add_dependencies(salmon_core libbwa)

+#add_dependencies(salmon_core libbwa)

 add_dependencies(salmon libbwa)

-add_dependencies(salmon_core libgff)

+#add_dependencies(salmon_core libgff)

 add_dependencies(salmon libgff)

-add_dependencies(salmon_core libdivsufsort)

+#add_dependencies(salmon_core libdivsufsort)

 add_dependencies(salmon libdivsufsort)

 # Link the executable

 target_link_libraries(unitTests

-    salmon_core

     gff

     ${PTHREAD_LIB}

     ${Boost_LIBRARIES}

@@ -259,7 +254,7 @@

 # 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

Description: redefine MEM_F_SELF_OVLP

 libbwa upstream has dropped MEM_F_SELF_OVLP in their commit 

 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this

 definition to fix an FTBFS.

Remark: This patch is deactivated since current source code

 builds nicely without it.

Author: Sascha Steinbiss <sascha@steinbiss.name>

--- a/src/SalmonQuantify.cpp

+++ b/src/SalmonQuantify.cpp

@@ -54,6 +54,7 @@ extern "C" {

 #include "ksort.h"

 #include "kvec.h"

 #include "utils.h"

+#define MEM_F_SELF_OVLP 0x40

 }

 // Jellyfish 2 include

@@ -126,6 +127,7 @@ extern "C" {

 #include "RapMapUtils.hpp"

 //#include "TextBootstrapWriter.hpp"

+

 /****** QUASI MAPPING DECLARATIONS *********/

 using MateStatus = rapmap::utils::MateStatus;

 using QuasiAlignment = rapmap::utils::QuasiAlignment;

Author: Michael R. Crusoe <crusoe@ucdavis.edu>

Description: Disable the newer version check

--- a/src/Salmon.cpp

+++ b/src/Salmon.cpp

@@ -208,10 +208,10 @@ int main(int argc, char* argv[]) {

       std::exit(0);

     }

-    if (!vm.count("no-version-check")) {

-      std::string versionMessage = getVersionMessage();

-      std::cout << versionMessage;

-    }

+    //if (!vm.count("no-version-check")) {

+    //  std::string versionMessage = getVersionMessage();

+    //  std::cout << versionMessage;

+    //}

     // po::notify(vm);

use_debian_packaged_libs.patch

disable-version-check.patch

# use-system-pkg-config-tbb.patch

# 0008-Remove-salmon_core-lib.patch

# add_MEM_F_SELF_OVLP.patch

Description: Use pkgconfig to find the system library for tbb

Remark: This patch is deactivated for the moment.

        use_debian_packaged_libs.patch is able to detect tbb

        and there is no point to fiddle around now any more.

        However, may be this is more elegant and the patch is

        left as documentation.

Author: Michael R. Crusoe <crusoe@ucdavis.edu>

--- a/CMakeLists.txt

+++ b/CMakeLists.txt

@@ -287,6 +287,9 @@ endif()

 set(Boost_USE_MULTITHREADED ON)

 #set(Boost_USE_STATIC_RUNTIME OFF)

+find_package (PkgConfig)

+pkg_check_modules(TBB REQUIRED tbb)

+

 find_package(ZLIB)

 if(NOT ZLIB_FOUND)

   message(FATAL_ERROR "zlib must be installed before configuration & building can proceed")