[med-svn] [spades] 04/09: adjust patches, links
Sascha Steinbiss
sascha at steinbiss.name
Mon Jun 6 22:54:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository spades.
commit 90622919cc419d423d00c8cc7432fd2cc9c09d82
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Mon Jun 6 22:22:23 2016 +0000
adjust patches, links
---
debian/changelog | 7 ++
debian/links | 4 ++
.../0002_use_debian_packaged_python-joblib.patch | 10 +--
debian/patches/0003_accept-system-bwa.patch | 12 ++--
.../0101_cmake_ignore_removed_python-yaml.patch | 13 +++-
.../0102_cmake_ignore_removed_python-joblib.patch | 6 +-
debian/patches/0110_build_single_thread.patch | 8 +--
debian/patches/0111_use_full_config_dirs.patch | 77 ++++++----------------
debian/patches/0113_adjust_paths.patch | 14 ++--
debian/patches/0114_use_debian_provided_libs.patch | 42 ++++++------
debian/patches/0115_enable_compiler_messages.patch | 4 +-
debian/patches/series | 3 +-
12 files changed, 89 insertions(+), 111 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index d092ab5..a652e26 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+spades (3.8.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Drop patches that are no longer necessary.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 05 Jun 2016 09:56:42 +0000
+
spades (3.7.1+dfsg-3) unstable; urgency=medium
* Force LANG and LANGUAGE to ensure reproducibility.
diff --git a/debian/links b/debian/links
index 0f2d0a6..2766c27 100644
--- a/debian/links
+++ b/debian/links
@@ -4,6 +4,10 @@ usr/bin/spades usr/bin/dipspades.py
usr/bin/spades usr/bin/dipspades
usr/bin/spades usr/bin/truspades.py
usr/bin/spades usr/bin/truspades
+usr/bin/spades usr/bin/metaspades.py
+usr/bin/spades usr/bin/metaspades
+usr/bin/spades usr/bin/plasmidspades.py
+usr/bin/spades usr/bin/plasmidspades
usr/bin/bwa usr/lib/spades/bin/bwa-spades
usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz
diff --git a/debian/patches/0002_use_debian_packaged_python-joblib.patch b/debian/patches/0002_use_debian_packaged_python-joblib.patch
index b1ce962..ade2763 100644
--- a/debian/patches/0002_use_debian_packaged_python-joblib.patch
+++ b/debian/patches/0002_use_debian_packaged_python-joblib.patch
@@ -7,9 +7,9 @@ Description: We are using Debian packaged python-joblib
The patch is non-intrusive since it conserves the original code and uses
Debian pyyaml only if the original method fails.
---- spades.orig/src/spades_pipeline/hammer_logic.py
-+++ spades/src/spades_pipeline/hammer_logic.py
-@@ -38,10 +38,13 @@
+--- a/src/spades_pipeline/hammer_logic.py
++++ b/src/spades_pipeline/hammer_logic.py
+@@ -42,10 +42,13 @@
support.sys_call([pigz_path, '-f', '-7', '-p', str(max_threads), reads_file], log)
else:
addsitedir(ext_python_modules_home)
@@ -27,8 +27,8 @@ Description: We are using Debian packaged python-joblib
n_jobs = min(len(to_compress), max_threads)
outputs = Parallel(n_jobs=n_jobs)(delayed(support.sys_call)(['gzip', '-f', '-7', reads_file]) for reads_file in to_compress)
for output in outputs:
---- spades.orig/src/spades_pipeline/lucigen_nxmate.py
-+++ spades/src/spades_pipeline/lucigen_nxmate.py
+--- a/src/spades_pipeline/lucigen_nxmate.py
++++ b/src/spades_pipeline/lucigen_nxmate.py
@@ -43,12 +43,14 @@
support.error("Can't process Lucigen NxMate reads! Python module regex is not installed!")
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index e015d2b..3ba7cc6 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.
---- spades.orig/src/spades_pipeline/support.py
-+++ spades/src/spades_pipeline/support.py
+--- a/src/spades_pipeline/support.py
++++ b/src/spades_pipeline/support.py
@@ -58,6 +58,22 @@
sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
sys.stdout.flush()
@@ -55,9 +55,9 @@ 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))
---- spades.orig/spades.py
-+++ spades/spades.py
-@@ -149,6 +149,22 @@
+--- a/spades.py
++++ b/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
-@@ -429,7 +445,11 @@
+@@ -443,7 +459,11 @@
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 d1b93fe..695befc 100644
--- a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
+++ b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
@@ -4,14 +4,21 @@ Description: Since we are using Debian packaged python-yaml
(see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
excluded
---- spades.orig/ext/src/CMakeLists.txt
-+++ spades/ext/src/CMakeLists.txt
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
@@ -4,8 +4,6 @@
add_subdirectory(nlopt)
add_subdirectory(python_libs/joblib2)
add_subdirectory(python_libs/joblib3)
-add_subdirectory(python_libs/pyyaml2)
-add_subdirectory(python_libs/pyyaml3)
- add_subdirectory(yaml-cpp)
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/0102_cmake_ignore_removed_python-joblib.patch b/debian/patches/0102_cmake_ignore_removed_python-joblib.patch
index 1a1a1cc..63177c1 100644
--- a/debian/patches/0102_cmake_ignore_removed_python-joblib.patch
+++ b/debian/patches/0102_cmake_ignore_removed_python-joblib.patch
@@ -4,14 +4,14 @@ Description: Since we are using Debian packaged python-joblib
(see 0002_use_debian_packaged_python-joblib.patch) the dir needs to be
excluded
---- spades.orig/ext/src/CMakeLists.txt
-+++ spades/ext/src/CMakeLists.txt
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
@@ -2,8 +2,6 @@
add_subdirectory(jemalloc)
add_subdirectory(nlopt)
-add_subdirectory(python_libs/joblib2)
-add_subdirectory(python_libs/joblib3)
- add_subdirectory(yaml-cpp)
add_subdirectory(ConsensusCore)
add_subdirectory(bamtools)
+ add_subdirectory(samtools)
diff --git a/debian/patches/0110_build_single_thread.patch b/debian/patches/0110_build_single_thread.patch
index bf0599a..5e28271 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 <sascha at steinbiss.name>
---- spades.orig/spades_compile.sh
-+++ spades/spades_compile.sh
+--- a/spades_compile.sh
++++ b/spades_compile.sh
@@ -20,6 +20,6 @@
set -e
- cd $BASEDIR/$BUILD_DIR
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$PREFIX $BASEDIR/src $*
+ cd "$BASEDIR/$BUILD_DIR"
+ cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$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 576e1c7..e6ccd68 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -2,31 +2,13 @@ Description: use full config include path
This patch makes sure that the config files are not dependent on local
directory structure.
Author: Sascha Steinbiss <sascha at steinbiss.name>
---- spades.orig/src/spades_pipeline/spades_logic.py
-+++ spades/src/spades_pipeline/spades_logic.py
-@@ -138,8 +138,18 @@
- dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
- # removing template configs
- for root, dirs, files in os.walk(dst_configs):
-+ replacements = {'#include "': ('#include "' + root + '/')}
- for cfg_file in files:
- cfg_file = os.path.join(root, cfg_file)
-+ lines = []
-+ with open(cfg_file) as infile:
-+ for line in infile:
-+ for src, target in replacements.iteritems():
-+ line = line.replace(src, target)
-+ lines.append(line)
-+ with open(cfg_file, 'w') as outfile:
-+ for line in lines:
-+ outfile.write(line)
- if cfg_file.endswith('.info.template'):
- if os.path.isfile(cfg_file.split('.template')[0]):
- os.remove(cfg_file)
-@@ -198,6 +208,18 @@
- dir_util.copy_tree(os.path.join(configs_dir, "debruijn"), dst_configs, preserve_times=False)
- # removing template configs
- for root, dirs, files in os.walk(dst_configs):
+--- a/src/spades_pipeline/spades_logic.py
++++ b/src/spades_pipeline/spades_logic.py
+@@ -179,6 +179,20 @@
+
+ add_configs(command, dst_configs)
+
++ for root, dirs, files in os.walk(dst_configs):
+ replacements = {'#include "': ('#include "' + root + '/')}
+ for cfg_file in files:
+ cfg_file = os.path.join(root, cfg_file)
@@ -39,15 +21,15 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
+ with open(cfg_file, 'w') as outfile:
+ for line in lines:
+ outfile.write(line)
- for cfg_file in files:
- cfg_file = os.path.join(root, cfg_file)
- if cfg_file.endswith('.info.template'):
---- spades.orig/src/spades_pipeline/corrector_logic.py
-+++ spades/src/spades_pipeline/corrector_logic.py
-@@ -51,6 +51,18 @@
- cfg_file_name = os.path.join(dst_configs, "corrector.info")
- # removing template configs
- for root, dirs, files in os.walk(dst_configs):
++
+ #print("Calling: " + " ".join(command))
+ support.sys_call(command, log)
+
+@@ -225,6 +239,19 @@
+ command = [os.path.join(execution_home, "scaffold_correction"), cfg_file_name]
+ add_configs(command, dst_configs)
+ log.info(str(command))
++ for root, dirs, files in os.walk(dst_configs):
+ replacements = {'#include "': ('#include "' + root + '/')}
+ for cfg_file in files:
+ cfg_file = os.path.join(root, cfg_file)
@@ -60,27 +42,6 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
+ with open(cfg_file, 'w') as outfile:
+ for line in lines:
+ outfile.write(line)
- for cfg_file in files:
- cfg_file = os.path.join(root, cfg_file)
- if cfg_file.endswith('.template'):
---- spades.orig/src/spades_pipeline/hammer_logic.py
-+++ spades/src/spades_pipeline/hammer_logic.py
-@@ -111,6 +111,18 @@
- cfg_file_name = os.path.join(dst_configs, "config.info")
- # removing template configs
- for root, dirs, files in os.walk(dst_configs):
-+ replacements = {'#include "': ('#include "' + root + '/')}
-+ for cfg_file in files:
-+ cfg_file = os.path.join(root, cfg_file)
-+ lines = []
-+ with open(cfg_file) as infile:
-+ for line in infile:
-+ for src, target in replacements.iteritems():
-+ line = line.replace(src, target)
-+ lines.append(line)
-+ with open(cfg_file, 'w') as outfile:
-+ for line in lines:
-+ outfile.write(line)
- for cfg_file in files:
- cfg_file = os.path.join(root, cfg_file)
- if cfg_file.endswith('.template'):
+ support.sys_call(command, log)
+
+
diff --git a/debian/patches/0113_adjust_paths.patch b/debian/patches/0113_adjust_paths.patch
index ea29a51..d4af7cc 100644
--- a/debian/patches/0113_adjust_paths.patch
+++ b/debian/patches/0113_adjust_paths.patch
@@ -2,8 +2,8 @@ Description: adjust runtime paths
Debian stores components od SPAdes in different places than expected by
upstream. This patch makes it look in the right locations.
Author: Sascha Steinbiss <sascha at steinbiss.name>
---- spades.orig/spades_init.py
-+++ spades/spades_init.py
+--- a/spades_init.py
++++ b/spades_init.py
@@ -25,7 +25,12 @@
global ext_python_modules_home
@@ -18,10 +18,10 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
install_prefix = os.path.dirname(spades_home)
bin_home = os.path.join(install_prefix, 'bin')
spades_home = os.path.join(install_prefix, 'share', 'spades')
---- spades.orig/truspades.py
-+++ spades/truspades.py
-@@ -11,8 +11,14 @@
- import sys
+--- a/truspades.py
++++ b/truspades.py
+@@ -13,8 +13,14 @@
+ import shutil
import spades_init
spades_init.init()
-truspades_home = spades_init.spades_home
@@ -37,7 +37,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
spades_version = spades_init.spades_version
import SeqIO # TODO: add to ext/scr/python_libs
-@@ -88,7 +94,7 @@
+@@ -90,7 +96,7 @@
def __call__(self, barcode_id):
reference_construction.CounstructSubreference(os.path.join(self.sam_dir, barcode_id + ".sam"), reference_construction.ReadReference(self.reference), os.path.join(self.result_dir, barcode_id))
return 0
diff --git a/debian/patches/0114_use_debian_provided_libs.patch b/debian/patches/0114_use_debian_provided_libs.patch
index c10a135..2fac37b 100644
--- a/debian/patches/0114_use_debian_provided_libs.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -8,19 +8,19 @@ 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 <sascha at steinbiss.name>
---- spades.orig/src/cmake/includes.cmake
-+++ spades/src/cmake/includes.cmake
+--- a/src/cmake/includes.cmake
++++ b/src/cmake/includes.cmake
@@ -3,6 +3,8 @@
set(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
+include_directories("/usr/include")
+include_directories(SYSTEM "/usr/include")
- include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR})
+ include_directories(${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}")
---- spades.orig/src/cmake/flags.cmake
-+++ spades/src/cmake/flags.cmake
+--- a/src/cmake/flags.cmake
++++ b/src/cmake/flags.cmake
@@ -53,3 +53,5 @@
if (SPADES_USE_TCMALLOC)
add_compile_options(-fno-omit-frame-pointer)
@@ -28,13 +28,22 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
+
+add_definitions(-DJEMALLOC_NO_DEMANGLE)
\ No newline at end of file
---- spades.orig/src/io/logger_impl.cpp
-+++ spades/src/io/logger_impl.cpp
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -1,6 +1,5 @@
+ # -*- cmake -*-
+
+-add_subdirectory(jemalloc)
+ add_subdirectory(nlopt)
+ add_subdirectory(ConsensusCore)
+ add_subdirectory(bamtools)
+--- a/src/modules/dev_support/logger/logger_impl.cpp
++++ b/src/modules/dev_support/logger/logger_impl.cpp
@@ -13,6 +13,7 @@
#include <vector>
- #include "logger/logger.hpp"
-+#include "memory_limit.hpp"
+ #include "dev_support/logger/logger.hpp"
++#include "dev_support/memory_limit.hpp"
#include "config.hpp"
@@ -58,22 +67,13 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
}
#else
void logger::log(level desired_level, const char* file, size_t line_num, const char* source, const char* msg) {
---- spades.orig/src/include/memory_limit.hpp
-+++ spades/src/include/memory_limit.hpp
-@@ -18,6 +18,7 @@
+--- a/src/modules/dev_support/memory_limit.hpp
++++ b/src/modules/dev_support/memory_limit.hpp
+@@ -20,6 +20,7 @@
#include <sys/resource.h>
#include "config.hpp"
+#include "verify.hpp"
#ifdef SPADES_USE_JEMALLOC
- # include <jemalloc/jemalloc.h>
---- spades.orig/ext/src/CMakeLists.txt
-+++ spades/ext/src/CMakeLists.txt
-@@ -1,6 +1,5 @@
- # -*- cmake -*-
--add_subdirectory(jemalloc)
- add_subdirectory(nlopt)
- add_subdirectory(yaml-cpp)
- add_subdirectory(ConsensusCore)
diff --git a/debian/patches/0115_enable_compiler_messages.patch b/debian/patches/0115_enable_compiler_messages.patch
index 7761754..b848157 100644
--- a/debian/patches/0115_enable_compiler_messages.patch
+++ b/debian/patches/0115_enable_compiler_messages.patch
@@ -2,8 +2,8 @@
+++ b/spades_compile.sh
@@ -20,6 +20,6 @@
set -e
- cd $BASEDIR/$BUILD_DIR
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$PREFIX $BASEDIR/src $*
+ cd "$BASEDIR/$BUILD_DIR"
+ cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" "$BASEDIR/src" $*
-make -j 1
+make -j 1 VERBOSE=1
make install
diff --git a/debian/patches/series b/debian/patches/series
index 72efd71..21d2e9e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -10,8 +10,7 @@
# use-debian-packaged-bamtools.patch ## <<-- does not work - see patch description
# use-debian-packaged-yaml-cpp.patch ## <<-- does not work - see patch description
0110_build_single_thread.patch
-0111_use_full_config_dirs.patch
-0112_spelling.patch
0113_adjust_paths.patch
0114_use_debian_provided_libs.patch
0115_enable_compiler_messages.patch
+0111_use_full_config_dirs.patch
--
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