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commit 109110e372b990796368d61d2328d015cd8e18fc Author: Sascha Steinbiss <[email protected]> Date: Sun Jul 24 10:05:16 2016 +0000 new upstream version --- debian/changelog | 7 +++++++ debian/copyright | 4 ++++ debian/patches/0003_accept-system-bwa.patch | 2 +- debian/patches/0103_use-debian-packaged-bwa.patch | 4 ++-- debian/patches/0111_use_full_config_dirs.patch | 4 ++-- debian/patches/0114_use_debian_provided_libs.patch | 2 +- debian/patches/0116_stable_link_order.patch | 2 +- 7 files changed, 18 insertions(+), 7 deletions(-) diff --git a/debian/changelog b/debian/changelog index 7dc517b..71aba26 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +spades (3.9.0+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + * Add copyright entry for cxxopts. + + -- Sascha Steinbiss <[email protected]> Sun, 24 Jul 2016 09:51:30 +0000 + spades (3.8.2+dfsg2-1) unstable; urgency=medium * Make sure bundled headers are not used by cleaning orig tarball. diff --git a/debian/copyright b/debian/copyright index 72bc13b..7225ba8 100644 --- a/debian/copyright +++ b/debian/copyright @@ -303,6 +303,10 @@ Files: ext/include/htrie/* Copyright: (c) 2011 Daniel C. Jones <[email protected]> License: MIT +Files: ext/include/cxxopts/* +Copyright: (c) 2014, 2015, 2016 Jarryd Beck +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 diff --git a/debian/patches/0003_accept-system-bwa.patch b/debian/patches/0003_accept-system-bwa.patch index 3ba7cc6..f89d04a 100644 --- a/debian/patches/0003_accept-system-bwa.patch +++ b/debian/patches/0003_accept-system-bwa.patch @@ -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 -@@ -443,7 +459,11 @@ +@@ -456,7 +472,11 @@ 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/0103_use-debian-packaged-bwa.patch b/debian/patches/0103_use-debian-packaged-bwa.patch index 91a0168..9355359 100644 --- a/debian/patches/0103_use-debian-packaged-bwa.patch +++ b/debian/patches/0103_use-debian-packaged-bwa.patch @@ -13,8 +13,8 @@ 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 ---- spades.orig/ext/tools/CMakeLists.txt -+++ spades/ext/tools/CMakeLists.txt +--- a/ext/tools/CMakeLists.txt ++++ b/ext/tools/CMakeLists.txt @@ -5,4 +5,3 @@ # See file LICENSE for details. ############################################################################ diff --git a/debian/patches/0111_use_full_config_dirs.patch b/debian/patches/0111_use_full_config_dirs.patch index 0807c62..50861da 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 <[email protected]> --- a/src/spades_pipeline/spades_logic.py +++ b/src/spades_pipeline/spades_logic.py -@@ -179,6 +179,20 @@ +@@ -180,6 +180,20 @@ add_configs(command, dst_configs) @@ -25,7 +25,7 @@ Author: Sascha Steinbiss <[email protected]> #print("Calling: " + " ".join(command)) support.sys_call(command, log) -@@ -226,6 +240,19 @@ +@@ -227,6 +241,19 @@ 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 812a66b..e66a3f8 100644 --- a/debian/patches/0114_use_debian_provided_libs.patch +++ b/debian/patches/0114_use_debian_provided_libs.patch @@ -89,7 +89,7 @@ Author: Sascha Steinbiss <[email protected]> @@ -9,4 +9,4 @@ add_library(graph_support STATIC - components/connected_component.cpp paths/bidirectional_path.cpp graph_support/scaff_supplementary.cpp) + 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 diff --git a/debian/patches/0116_stable_link_order.patch b/debian/patches/0116_stable_link_order.patch index f1e972f..73e4288 100644 --- a/debian/patches/0116_stable_link_order.patch +++ b/debian/patches/0116_stable_link_order.patch @@ -2,7 +2,7 @@ Description: use stable sort order for file globbing Author: Sascha Steinbiss <[email protected]> --- a/ext/src/llvm/CMakeLists.txt +++ b/ext/src/llvm/CMakeLists.txt -@@ -29,6 +29,7 @@ +@@ -26,6 +26,7 @@ ${SPADES_BUILT_INCLUDE_DIR}/llvm/Config.h) file(GLOB sources "[a-zA-Z]*.cpp" "[a-zA-Z]*.c") -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
