src/spades_pipeline/hammer_logic.py | 11 7 + 4 - 0 !
src/spades_pipeline/lucigen_nxmate.py | 12 7 + 5 - 0 !
2 files changed, 14 insertions(+), 9 deletions(-)

 we are using debian packaged python-joblib
 Debian has its own way to distinguish Python versions and there is no point
 in doing this inside the code.
 .
 The patch is non-intrusive since it conserves the original code and uses
 Debian pyyaml only if the original method fails.

spades.py | 22 21 + 1 - 0 !
src/spades_pipeline/support.py | 26 24 + 2 - 0 !
2 files changed, 45 insertions(+), 3 deletions(-)

 enable using debian packaged bwa instead of bwa-spades
 Users might have installed a local version of bwa which is used independently
 from SPAdes.  This is specifically true on Debian systems where the
 dependency system ensures the installation of bwa.  This patch uses the
 local installed bwa as fallback if bwa-spades is not found.
 .
 The patch is non-intrusive since it conserves the original code and uses
 Debian bwa only if bwa-spades is not available.
 .
 Note: The duplicated which() in two files is for sure not the best solution.
 In case you consider taking over the patch I'd suggest to take it over into
 some common import file.

ext/src/CMakeLists.txt | 4 1 + 3 - 0 !
1 file changed, 1 insertion(+), 3 deletions(-)

 since we are using debian packaged python-yaml
 (see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
 excluded

ext/src/CMakeLists.txt | 2 0 + 2 - 0 !
1 file changed, 2 deletions(-)

 since we are using debian packaged python-joblib
 (see 0002_use_debian_packaged_python-joblib.patch) the dir needs to be
 excluded

ext/tools/CMakeLists.txt | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 spades originally contained a code copy of bwa since the version
 of bwa which was current of the time of release did not builded with recent
 gcc versions.  Since this is not the case with Debian shipped bwa this code
 copy is skipped.
 .
 See https://lists.debian.org/debian-med/2014/02/msg00192.html
 .
 Note: I tried to patch the Python scripts which were calling bwa-spades to
 rather call /usr/bin/bwa but the test suite failed.  So as an alternative
 the package contains a symlink
    ln -s /usr/bin/bwa /usr/lib/spades/bin/bwa-spades
 which enables successfull run of the test suite

spades_compile.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 build in single thread
 Upstream builds this in 8 threads, which might overwhelm weaker machines.

spades_init.py | 9 7 + 2 - 0 !
truspades.py | 12 9 + 3 - 0 !
2 files changed, 16 insertions(+), 5 deletions(-)

 adjust runtime paths 

ext/src/CMakeLists.txt | 6 1 + 5 - 0 !
src/cmake/flags.cmake | 2 2 + 0 - 0 !
src/cmake/includes.cmake | 2 2 + 0 - 0 !
src/modules/algorithms/path_extend/overlap_analysis.hpp | 2 1 + 1 - 0 !
src/modules/assembly_graph/CMakeLists.txt | 2 1 + 1 - 0 !
src/modules/assembly_graph/graph_alignment/kmer_map.hpp | 2 1 + 1 - 0 !
src/modules/dev_support/logger/logger_impl.cpp | 10 6 + 4 - 0 !
src/modules/dev_support/memory_limit.hpp | 1 1 + 0 - 0 !
src/modules/math/kmer_coverage_model.cpp | 2 1 + 1 - 0 !
9 files changed, 16 insertions(+), 13 deletions(-)

 use debian-packaged jemalloc library 
 To improve building on non-amd64 archs, it is necessary to not
 use the unpatched libjemalloc copy bundled by upstream. This patch
 makes sure spades links against the packaged copy and no local
 version is built any more.

spades_compile.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable compiler messages 

src/spades_pipeline/spades_logic.py | 27 27 + 0 - 0 !
1 file changed, 27 insertions(+)

 use full config include path
 This patch makes sure that the config files are not dependent on local
 directory structure.

ext/src/llvm/CMakeLists.txt | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 use stable sort order for file globbing

spades_compile.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 enable building with debug symbols