[med-svn] [spades] 01/01: use Debian packaged LLVM

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a commit to branch debian_llvm
in repository spades.

commit 94b326151eba4671dc266ac0d2198596a9363c43
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue Jun 7 12:24:22 2016 +0000

    use Debian packaged LLVM
---
 debian/control                                     |  2 ++
 debian/patches/0114_use_debian_provided_libs.patch | 35 ++++++++++++++++++++--
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index b6fa378..c11730a 100644
--- a/debian/control
+++ b/debian/control
@@ -16,6 +16,8 @@ Build-Depends: debhelper (>= 9),
                libbamtools-dev,
                libjemalloc-dev,
                libhts-dev,
+               llvm-dev,
+               libnlopt-dev,
                python-yaml,
                python-joblib,
                asciidoctor (>= 1.5.3),
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 2fac37b..44ca524 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -30,13 +30,21 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 \ No newline at end of file
 --- a/ext/src/CMakeLists.txt
 +++ b/ext/src/CMakeLists.txt
-@@ -1,6 +1,5 @@
+@@ -1,12 +1,11 @@
  # -*- cmake -*-
  
 -add_subdirectory(jemalloc)
- add_subdirectory(nlopt)
+-add_subdirectory(nlopt)
++#add_subdirectory(nlopt)
  add_subdirectory(ConsensusCore)
  add_subdirectory(bamtools)
+ add_subdirectory(samtools)
+ add_subdirectory(cppformat)
+ add_subdirectory(ssw)
+ add_subdirectory(cityhash)
+-add_subdirectory(llvm)
++#add_subdirectory(llvm)
+ add_subdirectory(htrie)
 --- a/src/modules/dev_support/logger/logger_impl.cpp
 +++ b/src/modules/dev_support/logger/logger_impl.cpp
 @@ -13,6 +13,7 @@
@@ -77,3 +85,26 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  #ifdef SPADES_USE_JEMALLOC
  
+--- a/src/modules/pipeline/CMakeLists.txt
++++ b/src/modules/pipeline/CMakeLists.txt
+@@ -7,8 +7,19 @@
+ 
+ project(pipeline CXX)
+ 
++find_package(LLVM REQUIRED CONFIG)
++
++message(STATUS "Found LLVM ${LLVM_PACKAGE_VERSION}")
++message(STATUS "Using LLVMConfig.cmake in: ${LLVM_DIR}")
++
++include_directories(${LLVM_INCLUDE_DIRS})
++add_definitions(${LLVM_DEFINITIONS})
++
++llvm_map_components_to_libnames(llvm_libs support core object)
++message(STATUS "Using LLVM libs ${llvm_libs}")
++
+ add_library(pipeline STATIC
+             stage.cpp config_struct.cpp genomic_info_filler.cpp library.cpp)
+ 
+-target_link_libraries(pipeline input llvm-support)
++target_link_libraries(pipeline input ${llvm-libs})
+ 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git