[med-svn] [Git][med-team/kallisto][master] Update use_debian_packaged_htslib.patch

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
3786de08 by Andreas Tille at 2025-10-18T20:58:33+02:00
Update use_debian_packaged_htslib.patch

- - - - -


1 changed file:

- debian/patches/use_debian_packaged_htslib.patch


Changes:

=====================================
debian/patches/use_debian_packaged_htslib.patch
=====================================
@@ -23,9 +23,21 @@ Description: Adapt build system to Debian packaged libhts
  if (USE_BAM)
  ExternalProject_Add(htslib
      PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
-@@ -109,13 +118,13 @@ endif(ZLIBNG)
+@@ -107,15 +116,24 @@ if (ZLIBNG)
+ endif(ZLIBNG)
+ 
  if (USE_BAM)
- include_directories(${htslib_PREFIX}/src/htslib)
+-include_directories(${htslib_PREFIX}/src/htslib)
++    if(DEBIAN_BUILD)
++        # For Debian builds, use system htslib
++        find_package(PkgConfig REQUIRED)
++        pkg_check_modules(HTSLIB REQUIRED htslib)
++        include_directories(${HTSLIB_INCLUDE_DIRS})
++        link_libraries(${HTSLIB_LIBRARIES})
++    else()
++        # For non-Debian builds, use bundled htslib
++        include_directories(${htslib_PREFIX}/src/htslib)
++    endif()
  endif(USE_BAM)
 +endif()
  include_directories(${EXT_PROJECTS_DIR}/bifrost/build/src)
@@ -52,8 +64,20 @@ Description: Adapt build system to Debian packaged libhts
  
  if(NOT MAX_KMER_SIZE)
  set(MAX_KMER_SIZE "32")
-@@ -20,11 +22,16 @@ add_executable(kallisto main.cpp)
+@@ -18,13 +20,28 @@ target_include_directories(kallisto_core
+ 
+ add_executable(kallisto main.cpp)
  
++if (DEBIAN_BUILD)
++  if(USE_BAM)
++    # Link system htslib for Debian builds
++    find_package(PkgConfig REQUIRED)
++    pkg_check_modules(HTSLIB htslib)
++    target_link_libraries(kallisto ${HTSLIB_LIBRARIES})
++    target_link_libraries(kallisto_core ${HTSLIB_LIBRARIES})
++  endif()
++endif()
++
  find_package( Threads REQUIRED )
  ExternalProject_Get_Property(bifrost install_dir)
 +if(!DEBIAN_BUILD)
@@ -69,7 +93,7 @@ Description: Adapt build system to Debian packaged libhts
  
  if(LINK MATCHES static)
      set(BUILD_SHARED_LIBS OFF)
-@@ -94,4 +101,4 @@ else()
+@@ -94,4 +111,4 @@ else()
  endif(LINK MATCHES static)
  
  



View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/commit/3786de080c2e9d5726e9be40dab29ac8c6435662

-- 
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/commit/3786de080c2e9d5726e9be40dab29ac8c6435662
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