Commit 663dd0bb authored by Andreas Tille's avatar Andreas Tille
Browse files

Adapt build system to Debian packaged libhts

parent 7bd06402

debian/control

+2 −1
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@@ -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 → 100644
+1 −0
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use_debian_packaged_htslib.patch

debian/patches/use_debian_packaged_htslib.patch

0 → 100644
+55 −0
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Author: Andreas Tille <tille@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

+3 −4
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@@ -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