[med-svn] [Git][med-team/spoa][master] 4 commits: Link against zlib

Sat Jun 9 12:57:03 BST 2018

Andreas Tille pushed to branch master at Debian Med / spoa


Commits:
1045b079 by Andreas Tille at 2018-06-09T11:36:13+02:00
Link against zlib

- - - - -
4e651e83 by Andreas Tille at 2018-06-09T11:36:48+02:00
Create shared instead of static lib

- - - - -
58baa202 by Andreas Tille at 2018-06-09T13:53:10+02:00
Enable shared + static library

- - - - -
6ce0c36a by Andreas Tille at 2018-06-09T13:56:39+02:00
Additional library packages

- - - - -


6 changed files:

- debian/control
- debian/patches/series
- + debian/patches/shared_and_static.patch
- debian/patches/use_debian_packaged_libs.patch
- debian/rules
- + debian/spoa.install


Changes:

=====================================
debian/control
=====================================

--- a/debian/control
+++ b/debian/control
@@ -5,6 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
+               d-shlibs,
                libbioparser-dev
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/spoa
@@ -15,10 +16,41 @@ Package: spoa
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
-Description: SIMD partial order alignment tool/library
+Description: SIMD partial order alignment tool
  Spoa (SIMD POA) is a c++ implementation of the partial order alignment
  (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
  is used to generate consensus sequences (as described in
  10.1093/bioinformatics/btg109). It supports three alignment modes: local
  (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
  (overlap).
+
+Package: libspoa1.1.3
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: SIMD partial order alignment library
+ Spoa (SIMD POA) is a c++ implementation of the partial order alignment
+ (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
+ is used to generate consensus sequences (as described in
+ 10.1093/bioinformatics/btg109). It supports three alignment modes: local
+ (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
+ (overlap).
+ .
+ This package contains the shared library.
+
+Package: libspoa-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         libspoa1.1.3 (= ${binary:Version})
+Description: SIMD partial order alignment library (development files)
+ Spoa (SIMD POA) is a c++ implementation of the partial order alignment
+ (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
+ is used to generate consensus sequences (as described in
+ 10.1093/bioinformatics/btg109). It supports three alignment modes: local
+ (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
+ (overlap).
+ .
+ This package contains the static library and the header files.


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 use_debian_packaged_libs.patch
+shared_and_static.patch


=====================================
debian/patches/shared_and_static.patch
=====================================
--- /dev/null
+++ b/debian/patches/shared_and_static.patch
@@ -0,0 +1,31 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -16,9 +16,15 @@ option(spoa_build_executable "Build spoa
+ option(spoa_build_tests "Build spoa unit tests" OFF)
+ 
+ # build SPOA as a static library by default
+-set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
++# set(BUILD_SHARED_LIBS OFF CACHE BOOL "Build all libraries as shared")
+ 
+-add_library(spoa
++add_library(spoa SHARED
++    src/alignment_engine.cpp
++    src/graph.cpp
++    src/simd_alignment_engine.cpp
++    src/sisd_alignment_engine.cpp)
++
++add_library(spoa_static STATIC
+     src/alignment_engine.cpp
+     src/graph.cpp
+     src/simd_alignment_engine.cpp
+@@ -28,6 +34,10 @@ target_include_directories(spoa PUBLIC
+     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+     $<INSTALL_INTERFACE:include>)
+ 
++target_include_directories(spoa_static PUBLIC
++    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
++    $<INSTALL_INTERFACE:include>)
++
+ set_target_properties(spoa
+     PROPERTIES
+     VERSION ${spoa_VERSION}


=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
--- a/debian/patches/use_debian_packaged_libs.patch
+++ b/debian/patches/use_debian_packaged_libs.patch
@@ -13,7 +13,7 @@ Description: Use Debian packaged libraries
 -    endif()
 -
 -    target_link_libraries(spoa_bin spoa bioparser)
-+    target_link_libraries(spoa_bin spoa)
++    target_link_libraries(spoa_bin spoa z)
      set_target_properties(spoa_bin PROPERTIES OUTPUT_NAME spoa)
  
      install(TARGETS spoa_bin DESTINATION ${CMAKE_INSTALL_BINDIR})
@@ -27,5 +27,5 @@ Description: Use Debian packaged libraries
 -    add_subdirectory(vendor/googletest/googletest EXCLUDE_FROM_ALL)
 -
 -    target_link_libraries(spoa_test spoa bioparser gtest_main)
-+    target_link_libraries(spoa_test spoa )
++    target_link_libraries(spoa_test spoa z)
  endif(spoa_build_tests)


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,22 +1,23 @@
 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
 
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+DEB_CMAKE_EXTRA_FLAGS = -DCMAKE_BUILD_TYPE=Release \
+                        -Dspoa_build_executable=ON \
+                        -DBUILD_SHARED_LIBS=ON
 
 %:
 	dh $@
 
-#get-orig-source:
-#	. debian/get-orig-source
+override_dh_auto_configure:
+	dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS)
+
+override_dh_install:
+	dh_install
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --movedev debian/tmp/usr/include/* usr/include \
+		    --movedev debian/tmp/usr/lib/*/cmake usr/lib/$(DEB_HOST_MULTIARCH) \
+		    debian/tmp/usr/lib/*/*.so


=====================================
debian/spoa.install
=====================================
--- /dev/null
+++ b/debian/spoa.install
@@ -0,0 +1 @@
+usr/bin	usr



View it on GitLab: https://salsa.debian.org/med-team/spoa/compare/f4d7bced6ad06bba929aeb50b124f9cc74cf61d9...6ce0c36a32b696cc8e13e394a1c21b20c4a844bf

-- 
View it on GitLab: https://salsa.debian.org/med-team/spoa/compare/f4d7bced6ad06bba929aeb50b124f9cc74cf61d9...6ce0c36a32b696cc8e13e394a1c21b20c4a844bf
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