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tille pushed a commit to branch master
in repository rapmap.
commit 0dc5b71f401dd670ae00c6a142320bc11209da2a
Author: Andreas Tille <ti...@debian.org>
Date: Sat Oct 15 15:47:34 2016 +0200
Adapt patches
---
debian/patches/use-debian-libs.patch | 165 +++--------------------------------
1 file changed, 10 insertions(+), 155 deletions(-)
diff --git a/debian/patches/use-debian-libs.patch
b/debian/patches/use-debian-libs.patch
index 8ea793b..63ac2f8 100644
--- a/debian/patches/use-debian-libs.patch
+++ b/debian/patches/use-debian-libs.patch
@@ -4,7 +4,7 @@ Description: make RapMap use Debian's versions of dependencies
Author: Sascha Steinbiss <sas...@steinbiss.name>
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -160,32 +160,32 @@
+@@ -165,20 +165,6 @@ if (NOT ZLIB_FOUND)
endif()
@@ -22,54 +22,15 @@ Author: Sascha Steinbiss <sas...@steinbiss.name>
-)
-set(SUFFARRAY_INCLUDE_DIRS
${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-
--message("Build system will fetch and build SparseHash")
--message("==================================================================")
--ExternalProject_Add(libsparsehash
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L
https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o
sparsehash-2.0.2.tar.gz &&
-- tar -xzf sparsehash-2.0.2.tar.gz
-- SOURCE_DIR
${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
-- BUILD_IN_SOURCE TRUE
-- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
./configure --prefix=<INSTALL_DIR>"
-- INSTALL_COMMAND make install
--)
-+#message("Build system will build libdivsufsort")
-+#message("==================================================================")
-+#include(ExternalProject)
-+#ExternalProject_Add(libdivsufsort
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort.tar.gz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
-+# BINARY_DIR
${CMAKE_CURRENT_SOURCE_DIR}/external/libdivsufsort-master/build
-+# CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DBUILD_DIVSUFSORT64=TRUE -DUSE_OPENMP=TRUE -DBUILD_SHARED_LIBS=FALSE
-+#)
-+#set(SUFFARRAY_INCLUDE_DIRS
${CMAKE_CURRENT_SOURCE_DIR}/external/install/include)
-+
-+#message("Build system will fetch and build SparseHash")
-+#message("==================================================================")
-+#ExternalProject_Add(libsparsehash
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L
https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o
sparsehash-2.0.2.tar.gz &&
-+# tar -xzf sparsehash-2.0.2.tar.gz
-+# SOURCE_DIR
${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
-+# BUILD_IN_SOURCE TRUE
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER}
CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
-+# INSTALL_COMMAND make install
-+#)
-
-
if (NOT CEREAL_ROOT)
-@@ -220,24 +220,24 @@
+ set(CEREAL_ROOT ${GAT_SOURCE_DIR}/external/install)
+ endif()
+@@ -211,24 +197,7 @@ if (NOT JELLYFISH_ROOT)
set(JELLYFISH_ROOT ${GAT_SOURCE_DIR}/external/install)
endif()
-find_package(Jellyfish 2.2.5)
-+#find_package(Jellyfish 2.2.5)
-
+-
-if (NOT JELLYFISH_FOUND)
-message("Build system will fetch and build Jellyfish")
-message("==================================================================")
@@ -80,127 +41,21 @@ Author: Sascha Steinbiss <sas...@steinbiss.name>
- tar -xzvf jellyfish-2.2.5.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-- CONFIGURE_COMMAND
${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure
--prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+- CONFIGURE_COMMAND
${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure
--enable-shared=no --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER}
CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
CXXFLAGS=${JELLYFISH_CXX_FLAGS}
- BUILD_IN_SOURCE 1
- INSTALL_COMMAND make install
-)
-endif()
-+#if (NOT JELLYFISH_FOUND)
-+#message("Build system will fetch and build Jellyfish")
-+#message("==================================================================")
-+#ExternalProject_Add(libjellyfish
-+# DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-+# DOWNLOAD_COMMAND curl -k -L
https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
-o jellyfish-2.2.5.tgz &&
-+# rm -fr jellyfish-2.2.5 &&
-+# tar -xzvf jellyfish-2.2.5.tgz
-+# SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
-+# INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-+# CONFIGURE_COMMAND
${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure
--prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-+# BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-+# BUILD_IN_SOURCE 1
-+# INSTALL_COMMAND make install
-+#)
-+#endif()
++#find_package(Jellyfish 2.2.5)
set (FAST_MALLOC_LIB "")
set (HAVE_FAST_MALLOC FALSE)
---- a/include/RapMapUtils.hpp
-+++ b/include/RapMapUtils.hpp
-@@ -8,7 +8,7 @@
- #include <cereal/archives/binary.hpp>
- #include "jellyfish/mer_dna.hpp"
- #include "spdlog/spdlog.h"
--#include "spdlog/details/format.h"
-+#include "spdlog/fmt/bundled/format.h"
- #include "PairSequenceParser.hpp"
-
- #ifdef RAPMAP_SALMON_SUPPORT
-@@ -63,7 +63,7 @@
- std::string headerStr(hd.str());
- // Don't include the last '\n', since the logger will do it for
us.
- headerStr.pop_back();
-- out->info() << headerStr;
-+ out->info("%s", headerStr);
- }
-
- template <typename IndexT>
---- a/include/RapMapSAIndex.hpp
-+++ b/include/RapMapSAIndex.hpp
-@@ -7,7 +7,7 @@
- #include <cereal/archives/binary.hpp>
-
- #include "spdlog/spdlog.h"
--#include "spdlog/details/format.h"
-+#include "spdlog/fmt/bundled/format.h"
-
- #include "google/dense_hash_map"
- #include "bit_array.h"
---- a/src/RapMapMapper.cpp
-+++ b/src/RapMapMapper.cpp
-@@ -25,7 +25,9 @@
- #include "xxhash.h"
-
- #include "spdlog/spdlog.h"
--#include "spdlog/details/format.h"
-+#include "spdlog/fmt/bundled/format.h"
-+#include "spdlog/sinks/ostream_sink.h"
-+
-
- // Jellyfish 2 include
- #include "jellyfish/mer_dna.hpp"
-@@ -776,7 +778,7 @@
- // Get rid of last newline
- if (!outStr.empty()) {
- outStr.pop_back();
-- outQueue->info() << std::move(outStr);
-+ outQueue->info("%s", std::move(outStr));
- }
- sstream.clear();
- }
-@@ -889,7 +891,7 @@
- // Get rid of last newline
- if (!outStr.empty()){
- outStr.pop_back();
-- outQueue->info() << std::move(outStr);
-+ outQueue->info("%s", std::move(outStr));
- }
- sstream.clear();
- }
---- a/src/RapMapSAMapper.cpp
-+++ b/src/RapMapSAMapper.cpp
-@@ -32,7 +32,7 @@
-
- #include "spdlog/spdlog.h"
- #include "spdlog/sinks/ostream_sink.h"
--#include "spdlog/details/format.h"
-+#include "spdlog/fmt/bundled/format.h"
-
- // Jellyfish 2 include
- #include "jellyfish/mer_dna.hpp"
-@@ -176,7 +176,7 @@
- // Get rid of last newline
- if (!outStr.empty()) {
- outStr.pop_back();
-- outQueue->info() << std::move(outStr);
-+ outQueue->info("%s", std::move(outStr));
- }
- sstream.clear();
- /*
-@@ -297,7 +297,7 @@
- // Get rid of last newline
- if (!outStr.empty()) {
- outStr.pop_back();
-- outQueue->info() << std::move(outStr);
-+ outQueue->info("%s", std::move(outStr));
- }
- sstream.clear();
- /*
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -83,9 +83,12 @@
+@@ -84,9 +84,12 @@ set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/e
+ target_link_libraries(rapmap
${PTHREAD_LIB}
- #${Boost_LIBRARIES}
${ZLIB_LIBRARY}
- ${SUFFARRAY_LIB}
- ${SUFFARRAY64_LIB}
@@ -213,4 +68,4 @@ Author: Sascha Steinbiss <sas...@steinbiss.name>
+ jellyfish-2.0
m
${LIBLZMA_LIBRARIES}
- #${LIBSALMON_LINKER_FLAGS}
+ ${NON_APPLECLANG_LIBS}
--
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