[med-svn] [spades] 04/05: New upstream version 3.10.1
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 13:24:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository spades.
commit cf27ea5fa2a120b7f94b1005efc3d6e24dac5323
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Tue Apr 18 03:38:09 2017 -0700
New upstream version 3.10.1
refresh patches
fix boost bool cast
---
debian/changelog | 6 +
debian/control | 4 +-
debian/patches/0003_accept-system-bwa.patch | 10 +-
.../0101_cmake_ignore_removed_python-yaml.patch | 11 +-
debian/patches/0103_use-debian-packaged-bwa.patch | 11 +-
debian/patches/0110_build_single_thread.patch | 6 +-
debian/patches/0111_use_full_config_dirs.patch | 8 +-
debian/patches/0114_use_debian_provided_libs.patch | 185 ++++++++++++++-------
debian/patches/0115_enable_compiler_messages.patch | 6 +-
debian/patches/0116_stable_link_order.patch | 6 +-
debian/patches/0117_build_with_debug.patch | 8 +-
debian/patches/fix-bool-cast | 13 ++
debian/patches/series | 1 +
13 files changed, 182 insertions(+), 93 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index dea80e1..940d3ea 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+spades (3.10.1+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version 3.10.1+dfsg
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 18 Apr 2017 03:37:47 -0700
+
spades (3.9.1+dfsg-1) unstable; urgency=medium
* New upstream release.
diff --git a/debian/control b/debian/control
index e02d81e..832fbb4 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders:
Andreas Tille <tille at debian.org>,
Afif Elghraoui <afif at debian.org>,
- Sascha Steinbiss <satta at debian.org>
+ Sascha Steinbiss <satta at debian.org>,
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
@@ -23,6 +24,7 @@ Build-Depends: debhelper (>= 9),
python-joblib,
asciidoctor (>= 1.5.3),
bwa,
+ libbwa-dev,
lynx
Standards-Version: 3.9.8
Testsuite: autopkgtest
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index f89d04a..fa2e718 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -13,8 +13,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
---- a/src/spades_pipeline/support.py
-+++ b/src/spades_pipeline/support.py
+--- spades.orig/src/spades_pipeline/support.py
++++ spades/src/spades_pipeline/support.py
@@ -58,6 +58,22 @@
sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
sys.stdout.flush()
@@ -55,8 +55,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def check_file_existence(input_filename, message="", log=None, dipspades=False):
filename = abspath(expanduser(input_filename))
---- a/spades.py
-+++ b/spades.py
+--- spades.orig/spades.py
++++ spades/spades.py
@@ -156,6 +156,22 @@
print_value(cfg, "common", "max_memory", "Memory limit (in Gb)", " ")
log.info("")
@@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def fill_cfg(options_to_parse, log, secondary_filling=False):
skip_output_dir=secondary_filling
-@@ -456,7 +472,11 @@
+@@ -470,7 +486,11 @@
if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
cfg["mismatch_corrector"] = empty_config()
cfg["mismatch_corrector"].__dict__["skip-masked"] = None
diff --git a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
index 695befc..4dec147 100644
--- a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
+++ b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
@@ -4,8 +4,8 @@ Description: Since we are using Debian packaged python-yaml
(see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
excluded
---- a/ext/src/CMakeLists.txt
-+++ b/ext/src/CMakeLists.txt
+--- spades.orig/ext/src/CMakeLists.txt
++++ spades/ext/src/CMakeLists.txt
@@ -4,8 +4,6 @@
add_subdirectory(nlopt)
add_subdirectory(python_libs/joblib2)
@@ -15,10 +15,3 @@ Description: Since we are using Debian packaged python-yaml
add_subdirectory(ConsensusCore)
add_subdirectory(bamtools)
add_subdirectory(samtools)
-@@ -13,4 +11,4 @@
- add_subdirectory(ssw)
- add_subdirectory(cityhash)
- add_subdirectory(llvm)
--add_subdirectory(htrie)
-\ No newline at end of file
-+add_subdirectory(htrie)
diff --git a/debian/patches/0103_use-debian-packaged-bwa.patch b/debian/patches/0103_use-debian-packaged-bwa.patch
index 9355359..15a7233 100644
--- a/debian/patches/0103_use-debian-packaged-bwa.patch
+++ b/debian/patches/0103_use-debian-packaged-bwa.patch
@@ -13,10 +13,17 @@ Description: SPAdes originally contained a code copy of bwa since the version
ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
which enables successfull run of the test suite
---- a/ext/tools/CMakeLists.txt
-+++ b/ext/tools/CMakeLists.txt
+--- spades.orig/ext/tools/CMakeLists.txt
++++ spades/ext/tools/CMakeLists.txt
@@ -5,4 +5,3 @@
# See file LICENSE for details.
############################################################################
-add_subdirectory(bwa-0.7.12)
+--- spades.orig/ext/src/CMakeLists.txt
++++ spades/ext/src/CMakeLists.txt
+@@ -11,4 +11,3 @@
+ add_subdirectory(getopt_pp)
+ add_subdirectory(llvm)
+ add_subdirectory(htrie)
+-add_subdirectory(bwa)
diff --git a/debian/patches/0110_build_single_thread.patch b/debian/patches/0110_build_single_thread.patch
index 7b2b360..31fd94a 100644
--- a/debian/patches/0110_build_single_thread.patch
+++ b/debian/patches/0110_build_single_thread.patch
@@ -1,12 +1,12 @@
Description: build in single thread
Upstream builds this in 8 threads, which might overwhelm weaker machines.
Author: Sascha Steinbiss <satta at debian.org>
---- a/spades_compile.sh
-+++ b/spades_compile.sh
+--- spades.orig/spades_compile.sh
++++ spades/spades_compile.sh
@@ -20,6 +20,6 @@
set -e
cd "$BASEDIR/$BUILD_DIR"
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $*
+ cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src"
-make -j 8
+make -j 1
make install
diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index 50861da..5524172 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -2,9 +2,9 @@ Description: use full config include path
This patch makes sure that the config files are not dependent on local
directory structure.
Author: Sascha Steinbiss <satta at debian.org>
---- a/src/spades_pipeline/spades_logic.py
-+++ b/src/spades_pipeline/spades_logic.py
-@@ -180,6 +180,20 @@
+--- spades.orig/src/spades_pipeline/spades_logic.py
++++ spades/src/spades_pipeline/spades_logic.py
+@@ -185,6 +185,20 @@
add_configs(command, dst_configs)
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <satta at debian.org>
#print("Calling: " + " ".join(command))
support.sys_call(command, log)
-@@ -227,6 +241,19 @@
+@@ -232,6 +246,19 @@
command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
add_configs(command, dst_configs)
log.info(str(command))
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index e66a3f8..c48b267 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -8,8 +8,8 @@ Description: use Debian-packaged jemalloc library
does not report the 'stats.cactive_max' mallctl stat anymore.
Hence to avoid a NULL dereference the max rss value is logged.
Author: Sascha Steinbiss <satta at debian.org>
---- a/src/cmake/includes.cmake
-+++ b/src/cmake/includes.cmake
+--- spades.orig/src/cmake/includes.cmake
++++ spades/src/cmake/includes.cmake
@@ -3,6 +3,8 @@
set(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
@@ -19,8 +19,8 @@ Author: Sascha Steinbiss <satta at debian.org>
include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR} ${CMAKE_SOURCE_DIR} ${SPADES_MODULES_DIR})
include_directories(SYSTEM "${EXT_DIR}/include")
include_directories(SYSTEM "${ZLIB_INCLUDE_DIRS}")
---- a/src/cmake/flags.cmake
-+++ b/src/cmake/flags.cmake
+--- spades.orig/src/cmake/flags.cmake
++++ spades/src/cmake/flags.cmake
@@ -53,3 +53,5 @@
if (SPADES_USE_TCMALLOC)
add_compile_options(-fno-omit-frame-pointer)
@@ -28,29 +28,54 @@ Author: Sascha Steinbiss <satta at debian.org>
+
+add_definitions(-DJEMALLOC_NO_DEMANGLE)
\ No newline at end of file
---- a/ext/src/CMakeLists.txt
-+++ b/ext/src/CMakeLists.txt
-@@ -1,12 +1,8 @@
- # -*- cmake -*-
+--- spades.orig/src/common/assembly_graph/CMakeLists.txt
++++ spades/src/common/assembly_graph/CMakeLists.txt
+@@ -9,4 +9,4 @@
--add_subdirectory(jemalloc)
--add_subdirectory(nlopt)
- add_subdirectory(ConsensusCore)
--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
+ add_library(assembly_graph STATIC
+ components/connected_component.cpp paths/bidirectional_path.cpp paths/bidirectional_path_io/io_support.cpp paths/bidirectional_path_io/bidirectional_path_output.cpp graph_support/scaff_supplementary.cpp ../modules/alignment/edge_index_refiller.cpp graph_support/coverage_uniformity_analyzer.cpp)
+-target_link_libraries(assembly_graph hattrie)
++target_link_libraries(assembly_graph hat-trie)
+--- spades.orig/src/common/modules/alignment/kmer_map.hpp
++++ spades/src/common/modules/alignment/kmer_map.hpp
+@@ -9,7 +9,7 @@
+
+ #include "sequence/rtseq.hpp"
+
+-#include <htrie/hat-trie.h>
++#include <hat-trie/hat-trie.h>
+ #include <boost/iterator/iterator_facade.hpp>
+
+ namespace debruijn_graph {
+--- spades.orig/src/common/modules/path_extend/overlap_analysis.hpp
++++ spades/src/common/modules/path_extend/overlap_analysis.hpp
+@@ -2,7 +2,7 @@
+
+ #include "utils/logger/logger.hpp"
+ #include "utils/range.hpp"
+-#include "ssw/ssw_cpp.h"
++#include "ssw_cpp.h"
+
+ namespace debruijn_graph {
+ using omnigraph::Range;
+--- spades.orig/src/common/utils/coverage_model/kmer_coverage_model.cpp
++++ spades/src/common/utils/coverage_model/kmer_coverage_model.cpp
+@@ -18,7 +18,7 @@
+ #include <boost/math/distributions/geometric.hpp>
+ #include <boost/math/distributions/pareto.hpp>
+
+-#include <nlopt/nlopt.hpp>
++#include <nlopt.hpp>
+
+ #include <vector>
+
+--- spades.orig/src/common/utils/logger/logger_impl.cpp
++++ spades/src/common/utils/logger/logger_impl.cpp
@@ -13,6 +13,7 @@
#include <vector>
- #include "dev_support/logger/logger.hpp"
-+#include "dev_support/memory_limit.hpp"
+ #include "utils/logger/logger.hpp"
++#include "utils/memory_limit.hpp"
#include "config.hpp"
@@ -74,8 +99,8 @@ Author: Sascha Steinbiss <satta at debian.org>
}
#else
void logger::log(level desired_level, const char* file, size_t line_num, const char* source, const char* msg) {
---- a/src/modules/dev_support/memory_limit.hpp
-+++ b/src/modules/dev_support/memory_limit.hpp
+--- spades.orig/src/common/utils/memory_limit.hpp
++++ spades/src/common/utils/memory_limit.hpp
@@ -20,6 +20,7 @@
#include <sys/resource.h>
@@ -84,44 +109,86 @@ Author: Sascha Steinbiss <satta at debian.org>
#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 graph_alignment/edge_index_refiller.cpp)
--target_link_libraries(graph_support hattrie)
-+target_link_libraries(graph_support hat-trie)
---- a/src/modules/assembly_graph/graph_alignment/kmer_map.hpp
-+++ b/src/modules/assembly_graph/graph_alignment/kmer_map.hpp
-@@ -9,7 +9,7 @@
+--- spades.orig/src/projects/cclean/brute_force_clean.cpp
++++ spades/src/projects/cclean/brute_force_clean.cpp
+@@ -12,7 +12,7 @@
+ #include <iostream>
+
+ #include "adapter_index.hpp"
+-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
++#include "ssw_cpp.h" // Striped Smith-Waterman aligner
+ #include "additional.cpp"
+ #include "output.hpp"
+
+--- spades.orig/src/projects/cclean/job_wrappers.cpp
++++ spades/src/projects/cclean/job_wrappers.cpp
+@@ -13,7 +13,7 @@
+ #include "valid_kmer_generator.hpp"
+ #include "adapter_index.hpp"
+ #include "output.hpp"
+-#include "ssw/ssw_cpp.h"
++#include "ssw_cpp.h"
+ #include "utils.hpp"
- #include "data_structures/sequence/runtime_k.hpp"
+ using cclean_output::print_alignment;
+--- spades.orig/src/projects/cclean/main.cpp
++++ spades/src/projects/cclean/main.cpp
+@@ -21,7 +21,7 @@
--#include <htrie/hat-trie.h>
-+#include <hat-trie/hat-trie.h>
- #include <boost/iterator/iterator_facade.hpp>
-
- namespace debruijn_graph {
---- a/src/modules/math/kmer_coverage_model.cpp
-+++ b/src/modules/math/kmer_coverage_model.cpp
-@@ -18,7 +18,7 @@
- #include <boost/math/distributions/geometric.hpp>
- #include <boost/math/distributions/pareto.hpp>
+ #include "valid_kmer_generator.hpp"
+ #include "io/read_processor.hpp"
+-#include "modules/ssw_cpp.h"
++#include "ssw_cpp.h"
+ #include "additional.cpp"
+
+ #include "job_wrappers.hpp"
+--- spades.orig/src/projects/cclean/output.hpp
++++ spades/src/projects/cclean/output.hpp
+@@ -14,7 +14,7 @@
+ #include <io/read.hpp>
+ #include <ostream>
+ #include "comparator.hpp"
+-#include "modules/ssw_cpp.h"
++#include "ssw_cpp.h"
--#include <nlopt/nlopt.hpp>
-+#include <nlopt.hpp>
+ namespace cclean_output {
+--- spades.orig/src/projects/cclean/utils.cpp
++++ spades/src/projects/cclean/utils.cpp
+@@ -12,8 +12,7 @@
#include <vector>
---- a/src/modules/algorithms/path_extend/overlap_analysis.hpp
-+++ b/src/modules/algorithms/path_extend/overlap_analysis.hpp
-@@ -2,7 +2,7 @@
-
- #include "dev_support/logger/logger.hpp"
- #include "dev_support/range.hpp"
--#include "ssw/ssw_cpp.h"
-+#include "ssw_cpp.h"
+ #include "utils.hpp"
+-#include <ssw/ssw_cpp.h>
+-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
++#include <ssw_cpp.h> // Striped Smith-Waterman aligner
+ #include <io/read.hpp>
+ #include "additional.cpp"
+
+--- spades.orig/src/projects/cclean/utils.hpp
++++ spades/src/projects/cclean/utils.hpp
+@@ -8,7 +8,7 @@
+ #ifndef UTILS_HPP
+ #define UTILS_HPP
+
+-#include <ssw/ssw_cpp.h> // Striped Smith-Waterman aligner
++#include <ssw_cpp.h> // Striped Smith-Waterman aligner
+ #include <io/read.hpp>
+ #include "additional.cpp"
+ #include "running_modes.hpp"
+--- spades.orig/ext/src/CMakeLists.txt
++++ spades/ext/src/CMakeLists.txt
+@@ -1,13 +1,9 @@
+ # -*- cmake -*-
- namespace debruijn_graph {
- using omnigraph::Range;
+-add_subdirectory(jemalloc)
+-add_subdirectory(nlopt)
+ add_subdirectory(ConsensusCore)
+ add_subdirectory(bamtools)
+ add_subdirectory(samtools)
+ add_subdirectory(cppformat)
+-add_subdirectory(ssw)
+ add_subdirectory(cityhash)
+ add_subdirectory(getopt_pp)
+ add_subdirectory(llvm)
+-add_subdirectory(htrie)
diff --git a/debian/patches/0115_enable_compiler_messages.patch b/debian/patches/0115_enable_compiler_messages.patch
index 4a6eef7..3e3aa14 100644
--- a/debian/patches/0115_enable_compiler_messages.patch
+++ b/debian/patches/0115_enable_compiler_messages.patch
@@ -1,11 +1,11 @@
Description: enable compiler messages
Author: Sascha Steinbiss <satta at debian.org>
---- a/spades_compile.sh
-+++ b/spades_compile.sh
+--- spades.orig/spades_compile.sh
++++ spades/spades_compile.sh
@@ -20,6 +20,6 @@
set -e
cd "$BASEDIR/$BUILD_DIR"
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $*
+ cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src"
-make -j 1
+make -j 1 VERBOSE=1
make install
diff --git a/debian/patches/0116_stable_link_order.patch b/debian/patches/0116_stable_link_order.patch
index 73e4288..5cc8f95 100644
--- a/debian/patches/0116_stable_link_order.patch
+++ b/debian/patches/0116_stable_link_order.patch
@@ -1,8 +1,8 @@
Description: use stable sort order for file globbing
Author: Sascha Steinbiss <satta at debian.org>
---- a/ext/src/llvm/CMakeLists.txt
-+++ b/ext/src/llvm/CMakeLists.txt
-@@ -26,6 +26,7 @@
+--- spades.orig/ext/src/llvm/CMakeLists.txt
++++ spades/ext/src/llvm/CMakeLists.txt
+@@ -29,6 +29,7 @@
${SPADES_BUILT_INCLUDE_DIR}/llvm/Config.h)
file(GLOB sources "[a-zA-Z]*.cpp" "[a-zA-Z]*.c")
diff --git a/debian/patches/0117_build_with_debug.patch b/debian/patches/0117_build_with_debug.patch
index 08d2b83..b1a053f 100644
--- a/debian/patches/0117_build_with_debug.patch
+++ b/debian/patches/0117_build_with_debug.patch
@@ -1,13 +1,13 @@
Description: enable building with debug symbols
Author: Sascha Steinbiss <satta at debian.org>
---- a/spades_compile.sh
-+++ b/spades_compile.sh
+--- spades.orig/spades_compile.sh
++++ spades/spades_compile.sh
@@ -19,7 +19,7 @@
mkdir -p "$BASEDIR/$BUILD_DIR"
set -e
cd "$BASEDIR/$BUILD_DIR"
--cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $*
-+cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $*
+-cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src"
++cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_INSTALL_PREFIX="$PREFIX" $* "$BASEDIR/src"
make -j 1 VERBOSE=1
make install
cd $PREFIX
diff --git a/debian/patches/fix-bool-cast b/debian/patches/fix-bool-cast
new file mode 100644
index 0000000..2421ff3
--- /dev/null
+++ b/debian/patches/fix-bool-cast
@@ -0,0 +1,13 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Make explicit cast to bool
+--- spades.orig/src/common/func/pred.hpp
++++ spades/src/common/func/pred.hpp
+@@ -33,7 +33,7 @@
+ : data_(std::move(p)) { }
+
+ virtual bool operator()(T x) const override {
+- return data_(x);
++ return (bool) data_(x);
+ }
+
+ P data_;
diff --git a/debian/patches/series b/debian/patches/series
index f3d6337..4705406 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -16,3 +16,4 @@
0111_use_full_config_dirs.patch
0116_stable_link_order.patch
0117_build_with_debug.patch
+fix-bool-cast
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git
More information about the debian-med-commit
mailing list