[med-svn] [Git][med-team/kallisto][master] Adapt build system to Debian packaged libhts

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
663dd0bb by Andreas Tille at 2019-03-21T16:57:21Z
Adapt build system to Debian packaged libhts

- - - - -


4 changed files:

- debian/control
- + debian/patches/series
- + debian/patches/use_debian_packaged_htslib.patch
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -5,7 +5,8 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
                cmake,
-               libhdf5-dev
+               libhdf5-dev,
+               libhts-dev
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/kallisto
 Vcs-Git: https://salsa.debian.org/med-team/kallisto.git


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+use_debian_packaged_htslib.patch


=====================================
debian/patches/use_debian_packaged_htslib.patch
=====================================
@@ -0,0 +1,55 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 21 Mar 2019 15:53:04 +0100
+Description: Adapt build system to Debian packaged libhts
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -34,7 +34,7 @@ ELSE(LINK MATCHES shared)
+     message("shared build")
+ ENDIF(LINK MATCHES static)
+ 
+-
++if(!DEBIAN_BUILD)
+ include(ExternalProject)
+ ExternalProject_Add(htslib
+     PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+@@ -47,7 +47,7 @@ ExternalProject_Add(htslib
+ )
+ 
+ include_directories(${htslib_PREFIX}/src/htslib)
+-
++endif()
+ 
+ 
+ # add_compile_options(-Wdeprecated-register)
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -3,7 +3,9 @@ file(GLOB headers *.h *.hpp)
+ 
+ list(REMOVE_ITEM sources main.cpp)
+ 
++if(!DEBIAN_BUILD)
+ include_directories(../ext/htslib)
++endif()
+ 
+ add_library(kallisto_core ${sources} ${headers})
+ target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+@@ -11,7 +13,11 @@ target_include_directories(kallisto_core
+ add_executable(kallisto main.cpp)
+ 
+ find_package( Threads REQUIRED )
++if(DEBIAN_BUILD)
++target_link_libraries(kallisto kallisto_core pthread hts)
++else()
+ target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a)
++endif()
+ 
+ if(LINK MATCHES static)
+     set(BUILD_SHARED_LIBS OFF)
+@@ -56,4 +62,4 @@ else()
+ endif(LINK MATCHES static)
+ 
+ 
+-install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")
+\ No newline at end of file
++install(TARGETS kallisto DESTINATION "${CMAKE_INSTALL_BINDIR}")


=====================================
debian/rules
=====================================
@@ -20,12 +20,11 @@ include /usr/share/dpkg/default.mk
 %:
 	dh $@
 
+override_dh_auto_configure:
+	dh_auto_configure -- -DDEBIAN_BUILD=1
+
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 #override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 #	do_stuff_for_testing
 #endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source



View it on GitLab: https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d

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View it on GitLab: https://salsa.debian.org/med-team/kallisto/commit/663dd0bb6d300661c9d9ddd4972198f35440e10d
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