[med-svn] [spades] 01/01: stop using embedded libssw, , libhat-trie and libnlopt

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 7796befbf03d50c95557bba3fc888b830a2dee6f
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Jun 28 08:44:00 2016 +0000

    stop using embedded libssw,, libhat-trie and libnlopt
---
 debian/control                                     |  8 +++++++-
 debian/patches/0114_use_debian_provided_libs.patch | 21 ++++++++++++++++++---
 2 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/debian/control b/debian/control
index b6fa378..e40bf5b 100644
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,10 @@ Build-Depends: debhelper (>= 9),
                libbam-dev,
                libbamtools-dev,
                libjemalloc-dev,
+               libhat-trie-dev,
                libhts-dev,
+               libnlopt-dev,
+               libssw-dev,
                python-yaml,
                python-joblib,
                asciidoctor (>= 1.5.3),
@@ -37,7 +40,10 @@ Depends: ${shlibs:Depends},
          bwa,
          bamtools,
          samtools,
-         libjemalloc1
+         libjemalloc1,
+         libnlopt0,
+         libhat-trie0,
+         libssw0
 Description: genome assembler for single-cell and isolates data sets
  The SPAdes – St. Petersburg genome assembler is intended for both
  standard isolates and single-cell MDA bacteria assemblies.  It works
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index 2fac37b..28ec2a5 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -30,13 +30,20 @@ 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 +1,8 @@
  # -*- cmake -*-
  
 -add_subdirectory(jemalloc)
- add_subdirectory(nlopt)
+-add_subdirectory(nlopt)
  add_subdirectory(ConsensusCore)
- add_subdirectory(bamtools)
+-add_subdirectory(bamtools)
+ add_subdirectory(samtools)
++add_subdirectory(bamtools)
+ add_subdirectory(cppformat)
+-add_subdirectory(ssw)
+ add_subdirectory(cityhash)
+ 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 +84,11 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  #ifdef SPADES_USE_JEMALLOC
  
+--- a/src/modules/assembly_graph/CMakeLists.txt
++++ b/src/modules/assembly_graph/CMakeLists.txt
+@@ -9,4 +9,4 @@
+ 
+ add_library(graph_support STATIC
+             components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp)
+-target_link_libraries(graph_support hattrie)
++target_link_libraries(graph_support hat-trie)

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