[med-svn] [Git][med-team/metabat][master] Apply patch by Alexis Murzeau <amubtdx at gmail.com>

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / metabat


Commits:
5bc8c775 by Andreas Tille at 2020-05-29T10:03:14+02:00
Apply patch by Alexis Murzeau <amubtdx at gmail.com>

- - - - -


1 changed file:

- debian/patches/use_debian_packaged_libs.patch


Changes:

=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,6 +1,12 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
+Date: Thu, 28 May 2020 21:21:02 +0200
+Subject: Use Debian packaged libraries
+
 Last-Update: Thu, 28 May 2020 17:21:42 +0200
-Description: Use Debian packaged libraries
+---
+ CMakeLists.txt     | 15 ++++++++++++---
+ src/CMakeLists.txt |  8 ++++----
+ 2 files changed, 16 insertions(+), 7 deletions(-)
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
@@ -17,32 +23,51 @@ Description: Use Debian packaged libraries
  
  set(CMAKE_CXX_STANDARD 11)
  set(CMAKE_CXX_STANDARD_REQUIRED ON)
-@@ -23,7 +25,7 @@ add_definitions(-D_XOPEN_SOURCE=700)
+@@ -23,7 +25,13 @@ add_definitions(-D_XOPEN_SOURCE=700)
  
  set(PRE_CONFIGURE_FILE "metabat_version.h.in")
  set(POST_CONFIGURE_FILE "metabat_version.h")
 -include(cmake/git-watcher.cmake)
 +# include(cmake/git-watcher.cmake)
++set(GIT_RETRIEVED_STATE "")
++set(GIT_HEAD_SHA1 "nosha")
++set(GIT_IS_DIRTY 0)
++set(BUILD_TIMESTAMP 0)
++configure_file("${PRE_CONFIGURE_FILE}" "${POST_CONFIGURE_FILE}" @ONLY)
++include_directories("${CMAKE_CURRENT_BINARY_DIR}")
  
  if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
    # using Clang
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -36,7 +36,7 @@ set(targets metabat1 metabat2)
+@@ -4,6 +4,8 @@ set(Boost_USE_STATIC_LIBS   ON)
+ find_package(Boost 1.55.0 COMPONENTS program_options filesystem system graph serialization iostreams REQUIRED)
+ include_directories( ${Boost_INCLUDE_DIRS} )
+ 
++include_directories( ${HTSlib_INCLUDE_DIRS} )
++
+ # find and use OpenMP
+ find_package(OpenMP)
+ 
+@@ -36,8 +38,8 @@ set(targets metabat1 metabat2)
  foreach(target ${targets})
  
     add_executable(${target} ${target}.cpp)
 -   add_dependencies(${target} htslib zlib check_git_repository)
+-   target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) 
 +   add_dependencies(${target} htslib zlib)
-    target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) 
++   target_link_libraries(${target} ${HTSlib_LIBRARIES} ZLIB::ZLIB ${Boost_LIBRARIES} ${EXTRALIBS} )
  
  endforeach()
-@@ -48,7 +48,7 @@ install(TARGETS ${targets}
+ 
+@@ -48,8 +50,8 @@ install(TARGETS ${targets}
  set(targets jgi_summarize_bam_contig_depths contigOverlaps)
  foreach(target ${targets})
     add_executable(${target} ${target}.cpp)
 -   add_dependencies(${target} htslib zlib check_git_repository)
+-   target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) 
 +   add_dependencies(${target} htslib zlib)
-    target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) 
++   target_link_libraries(${target} ${HTSlib_LIBRARIES} ZLIB::ZLIB ${Boost_LIBRARIES} )
  endforeach()
  
+ 



View it on GitLab: https://salsa.debian.org/med-team/metabat/-/commit/5bc8c77590ca3898ae4fc9e0bc61d44edfdbe273

-- 
View it on GitLab: https://salsa.debian.org/med-team/metabat/-/commit/5bc8c77590ca3898ae4fc9e0bc61d44edfdbe273
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