[med-svn] [snpomatic] 08/15: add patches

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository snpomatic.

commit d0e4a229af2bc0778ca35b6384503e61bab68784
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Dec 12 21:18:55 2015 +0000

    add patches
---
 debian/patches/build_all_binaries | 11 +++++++++++
 debian/patches/hardening          | 31 +++++++++++++++++++++++++++++++
 debian/patches/series             |  2 ++
 3 files changed, 44 insertions(+)

diff --git a/debian/patches/build_all_binaries b/debian/patches/build_all_binaries
new file mode 100644
index 0000000..83ed7d5
--- /dev/null
+++ b/debian/patches/build_all_binaries
@@ -0,0 +1,11 @@
+--- a/Makefile
++++ b/Makefile
+@@ -8,7 +8,7 @@
+ #CXXFLAGS=-g -O2 -ip -align -falign-functions -Wno-deprecated -Isrc -w
+ #LIBS=
+ 
+-
++all: findknownsnps reassemble variety mapcontigs ungap
+ 
+ findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+ 	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..38c5326
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,31 @@
+--- a/Makefile
++++ b/Makefile
+@@ -11,22 +11,22 @@
+ 
+ 
+ findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
+ 
+ reassemble: src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
+ 
+ variety: src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
+ 
+ mapcontigs: src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
+ 
+ ungap: src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
+-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) $(LIBS) $^ -o $@
+ 
+ .cpp.o:
+-	$(CXX) $(CXXFLAGS) -c $< -o $@
++	$(CXX) $(CFLAGS) $(CXXFLAGS) -c $< -o $@
+ 
+ clean:
+ 	rm -f *.o
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8cf2dc3
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+hardening
+build_all_binaries

-- 
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