[med-svn] [rapmap] 02/02: use Debian's dependencies
Sascha Steinbiss
satta at debian.org
Tue Sep 6 20:16:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository rapmap.
commit 78d6e5dfc7431f70aa1655edab1fe6397c29cdf5
Author: Sascha Steinbiss <satta at debian.org>
Date: Tue Sep 6 20:15:56 2016 +0000
use Debian's dependencies
---
debian/patches/series | 1 +
debian/patches/use-debian-libs.patch | 216 +++++++++++++++++++++++++++++++++++
2 files changed, 217 insertions(+)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..621280c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use-debian-libs.patch
diff --git a/debian/patches/use-debian-libs.patch b/debian/patches/use-debian-libs.patch
new file mode 100644
index 0000000..8ea793b
--- /dev/null
+++ b/debian/patches/use-debian-libs.patch
@@ -0,0 +1,216 @@
+Description: make RapMap use Debian's versions of dependencies
+ This involves disabling downloads and adjusting API usage to the versions
+ packaged in Debian.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -160,32 +160,32 @@
+ endif()
+
+
+-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
+-)
++#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(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("==================================================================")
+-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()
++#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()
+
+ 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 @@
+ ${PTHREAD_LIB}
+ #${Boost_LIBRARIES}
+ ${ZLIB_LIBRARY}
+- ${SUFFARRAY_LIB}
+- ${SUFFARRAY64_LIB}
+- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
++ #${SUFFARRAY_LIB}
++ #${SUFFARRAY64_LIB}
++ #${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a
++ divsufsort
++ divsufsort64
++ jellyfish-2.0
+ m
+ ${LIBLZMA_LIBRARIES}
+ #${LIBSALMON_LINKER_FLAGS}
--
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