[med-svn] [spades] 05/07: new upstream release
Sascha Steinbiss
sascha at steinbiss.name
Wed Feb 24 22:08:45 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 3ea0a5900b9cbe8c626ff61f8e672aca42cf214b
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Wed Feb 24 21:57:36 2016 +0000
new upstream release
---
debian/changelog | 8 ++--
debian/copyright | 49 ++++++++++++++++++----
.../0001_use_debian_packaged_python-yaml.patch | 8 ++--
debian/patches/0003_accept-system-bwa.patch | 4 +-
.../0101_cmake_ignore_removed_python-yaml.patch | 2 +-
debian/patches/0111_use_full_config_dirs.patch | 6 +--
debian/patches/0112_spelling.patch | 13 +-----
debian/patches/0113_adjust_paths.patch | 35 +++++++++++-----
...c.patch => 0114_use_debian_provided_libs.patch} | 24 ++++-------
debian/patches/series | 2 +-
10 files changed, 92 insertions(+), 59 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 435a96d..793a6a6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,10 @@
-spades (3.6.2+dfsg-3) UNRELEASED; urgency=medium
+spades (3.7.0+dfsg-1) UNRELEASED; urgency=medium
- * make changelog building reproducible
+ * Make changelog building reproducible.
+ * New upstream release.
+ * Update d/copyright.
- -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 22 Feb 2016 21:14:51 +0000
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 24 Feb 2016 19:21:40 +0000
spades (3.6.2+dfsg-2) unstable; urgency=medium
diff --git a/debian/copyright b/debian/copyright
index 06143bd..d1fa376 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -17,6 +17,10 @@ Files-Excluded:
ext/src/samtools/bcftools/bcftools
ext/src/samtools/win32
src/include/md5.h
+ ext/include/jemalloc
+ ext/src/jemalloc
+ *__pycache__*
+ *.pyc
Files: *
Copyright: 2011-2014 Saint-Petersburg Academic University
@@ -164,6 +168,39 @@ Comment:
This is packaged in Debian as python-pbconsensuscore, but only the python
bindings are packaged.
+Files: ext/include/llvm/*
+Copyright: (c) 2003-2015 University of Illinois at Urbana-Champaign.
+ All rights reserved.
+License: UoI-NCSA
+
+License: UoI-NCSA
+ Permission is hereby granted, free of charge, to any person obtaining a copy of
+ this software and associated documentation files (the "Software"), to deal with
+ the Software without restriction, including without limitation the rights to
+ use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+ of the Software, and to permit persons to whom the Software is furnished to do
+ so, subject to the following conditions:
+ .
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimers.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimers in the
+ documentation and/or other materials provided with the distribution.
+ .
+ * Neither the names of the LLVM Team, University of Illinois at
+ Urbana-Champaign, nor the names of its contributors may be used to
+ endorse or promote products derived from this Software without specific
+ prior written permission.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE
+ SOFTWARE.
+
Files: ext/include/bamtools/*
ext/src/bamtools/*
Copyright: (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
@@ -257,6 +294,11 @@ Comment:
The original license can be found at:
https://github.com/jbeder/yaml-cpp/blob/master/LICENSE
+Files: ext/include/city/*
+ ext/src/cityhash/*
+Copyright: (c) 2011 Google, Inc.
+License: MIT
+
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
@@ -308,13 +350,6 @@ Copyright: (c) 2015 Saint Petersburg State University
(c) 2011 Dmitry Vyukov. All rights reserved.
License: BSD-2-clause
-Files: ext/include/jemalloc/*
- ext/src/jemalloc/*
-Copyright: (C) 2002-2015 Jason Evans <jasone at canonware.com>. All rights reserved.
- (C) 2007-2012 Mozilla Foundation. All rights reserved.
- (C) 2009-2015 Facebook, Inc. All rights reserved.
-License: BSD-2-clause
-
License: BSD-2-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
diff --git a/debian/patches/0001_use_debian_packaged_python-yaml.patch b/debian/patches/0001_use_debian_packaged_python-yaml.patch
index 0389734..8cba706 100644
--- a/debian/patches/0001_use_debian_packaged_python-yaml.patch
+++ b/debian/patches/0001_use_debian_packaged_python-yaml.patch
@@ -23,7 +23,7 @@ Description: We are using Debian packaged python-yaml
import alignment
--- a/src/spades_pipeline/hammer_logic.py
+++ b/src/spades_pipeline/hammer_logic.py
-@@ -74,10 +74,7 @@
+@@ -76,10 +76,7 @@
def prepare_config_ih(filename, cfg, ext_python_modules_home):
addsitedir(ext_python_modules_home)
@@ -35,7 +35,7 @@ Description: We are using Debian packaged python-yaml
data = pyyaml.load(open(filename, 'r'))
data["dataset"] = cfg.dataset_yaml_filename
-@@ -91,10 +88,13 @@
+@@ -93,10 +90,13 @@
def run_hammer(corrected_dataset_yaml_filename, configs_dir, execution_home, cfg,
not_used_dataset_data, ext_python_modules_home, log):
addsitedir(ext_python_modules_home)
@@ -53,7 +53,7 @@ Description: We are using Debian packaged python-yaml
dst_configs = os.path.join(cfg.output_dir, "configs")
if os.path.exists(dst_configs):
shutil.rmtree(dst_configs)
-@@ -143,4 +143,4 @@
+@@ -145,4 +145,4 @@
log.info("\n== Dataset description file was created: " + corrected_dataset_yaml_filename + "\n")
if os.path.isdir(cfg.tmp_dir):
@@ -62,7 +62,7 @@ Description: We are using Debian packaged python-yaml
+ shutil.rmtree(cfg.tmp_dir)
--- a/src/spades_pipeline/spades_logic.py
+++ b/src/spades_pipeline/spades_logic.py
-@@ -69,10 +69,7 @@
+@@ -70,10 +70,7 @@
max_read_length = 0
if os.path.isfile(est_params_filename):
addsitedir(ext_python_modules_home)
diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch
index 087b47b..00f1ac4 100644
--- a/debian/patches/0003_accept-system-bwa.patch
+++ b/debian/patches/0003_accept-system-bwa.patch
@@ -57,7 +57,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
filename = abspath(expanduser(input_filename))
--- a/spades.py
+++ b/spades.py
-@@ -144,6 +144,22 @@
+@@ -146,6 +146,22 @@
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
-@@ -415,7 +431,11 @@
+@@ -426,7 +442,11 @@
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 d834cf7..30415e2 100644
--- a/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
+++ b/debian/patches/0101_cmake_ignore_removed_python-yaml.patch
@@ -6,7 +6,7 @@ Description: Since we are using Debian packaged python-yaml
--- a/ext/src/CMakeLists.txt
+++ b/ext/src/CMakeLists.txt
-@@ -4,8 +4,6 @@ add_subdirectory(jemalloc)
+@@ -4,8 +4,6 @@
add_subdirectory(nlopt)
add_subdirectory(python_libs/joblib2)
add_subdirectory(python_libs/joblib3)
diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch
index fa4ec01..2a5ac61 100644
--- a/debian/patches/0111_use_full_config_dirs.patch
+++ b/debian/patches/0111_use_full_config_dirs.patch
@@ -4,7 +4,7 @@ Description: use full config include path
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/spades_pipeline/spades_logic.py
+++ b/src/spades_pipeline/spades_logic.py
-@@ -134,8 +134,18 @@
+@@ -135,8 +135,18 @@
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):
@@ -23,7 +23,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
if cfg_file.endswith('.info.template'):
if os.path.isfile(cfg_file.split('.template')[0]):
os.remove(cfg_file)
-@@ -194,6 +204,18 @@
+@@ -195,6 +205,18 @@
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):
@@ -65,7 +65,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
if cfg_file.endswith('.template'):
--- a/src/spades_pipeline/hammer_logic.py
+++ b/src/spades_pipeline/hammer_logic.py
-@@ -109,6 +109,18 @@
+@@ -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):
diff --git a/debian/patches/0112_spelling.patch b/debian/patches/0112_spelling.patch
index 9e4b617..893346c 100644
--- a/debian/patches/0112_spelling.patch
+++ b/debian/patches/0112_spelling.patch
@@ -53,7 +53,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
}
--- a/src/debruijn/pacbio/pac_index.hpp
+++ b/src/debruijn/pacbio/pac_index.hpp
-@@ -585,7 +585,7 @@
+@@ -534,7 +534,7 @@
|| !IsConsistent(s, *(iter->second),
*(next_iter->second))) {
if (next_iter != cur_cluster.end()) {
@@ -76,14 +76,3 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first));
TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second));
edge1 = split_edges.first;
---- a/src/debruijn/simplification.cpp
-+++ b/src/debruijn/simplification.cpp
-@@ -91,7 +91,7 @@
- INFO("Average coverage = " << cfg::get().ds.avg_coverage());
- if (!cfg::get().ds.single_cell) {
- if (cfg::get().ds.avg_coverage() < gp.ginfo.ec_bound())
-- WARN("The determined errorneous connection coverage threshold may be determined improperly\n");
-+ WARN("The determined erroneous connection coverage threshold may be determined improperly\n");
- }
- }
-
diff --git a/debian/patches/0113_adjust_paths.patch b/debian/patches/0113_adjust_paths.patch
index 4118064..280e62e 100644
--- a/debian/patches/0113_adjust_paths.patch
+++ b/debian/patches/0113_adjust_paths.patch
@@ -20,16 +20,29 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
spades_home = os.path.join(install_prefix, 'share', 'spades')
--- a/truspades.py
+++ b/truspades.py
-@@ -14,7 +14,11 @@
- bin_home = os.path.join(truspades_home, 'bin')
- python_modules_home = os.path.join(truspades_home, 'src')
-
--if os.path.isfile(os.path.join(truspades_home, 'spades')):
+@@ -11,8 +11,14 @@
+ import sys
+ import spades_init
+ spades_init.init()
+-truspades_home = spades_init.spades_home
+-spades_home = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
++
+if os.path.isfile('/usr/lib/spades/bin/spades'):
-+ bin_home = '/usr/lib/spades/bin/'
+ truspades_home = '/usr/share/spades'
-+ python_modules_home = truspades_home
-+elif os.path.isfile(os.path.join(truspades_home, 'spades')):
- install_prefix = os.path.dirname(truspades_home)
- bin_home = os.path.join(install_prefix, 'bin')
- truspades_home = os.path.join(install_prefix, 'share', 'spades')
++ spades_home = '/usr/lib/spades/bin/'
++else:
++ truspades_home = spades_init.spades_home
++ spades_home = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
++
+ spades_version = spades_init.spades_version
+
+ import SeqIO # TODO: add to ext/scr/python_libs
+@@ -88,7 +94,7 @@
+ 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
+-
++
+ def ConstructSubreferences(dataset, options):
+ reference_construction.ConstructSubreferences(dataset, options.reference, options.output_dir, options.index, options.threads, log = None)
+
diff --git a/debian/patches/0114_use_debian_provided_jemalloc.patch b/debian/patches/0114_use_debian_provided_libs.patch
similarity index 94%
rename from debian/patches/0114_use_debian_provided_jemalloc.patch
rename to debian/patches/0114_use_debian_provided_libs.patch
index 9d5e172..234dd47 100644
--- a/debian/patches/0114_use_debian_provided_jemalloc.patch
+++ b/debian/patches/0114_use_debian_provided_libs.patch
@@ -8,21 +8,6 @@ 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>
---- a/ext/src/CMakeLists.txt
-+++ b/ext/src/CMakeLists.txt
-@@ -1,10 +1,9 @@
- # -*- cmake -*-
-
--add_subdirectory(jemalloc)
- add_subdirectory(nlopt)
- add_subdirectory(yaml-cpp)
- add_subdirectory(ConsensusCore)
- add_subdirectory(bamtools)
- add_subdirectory(samtools)
- add_subdirectory(cppformat)
--add_subdirectory(ssw)
-\ No newline at end of file
-+add_subdirectory(ssw)
--- a/src/cmake/includes.cmake
+++ b/src/cmake/includes.cmake
@@ -3,6 +3,8 @@
@@ -83,3 +68,12 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
#ifdef SPADES_USE_JEMALLOC
# include <jemalloc/jemalloc.h>
+--- a/ext/src/CMakeLists.txt
++++ b/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/series b/debian/patches/series
index 61c25b1..9f945d8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -14,4 +14,4 @@
0111_use_full_config_dirs.patch
0112_spelling.patch
0113_adjust_paths.patch
-0114_use_debian_provided_jemalloc.patch
+0114_use_debian_provided_libs.patch
--
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