Author: osallou
Date: 2014-08-18 17:11:41 +0000 (Mon, 18 Aug 2014)
New Revision: 17770
Added:
trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
Modified:
trunk/packages/mapsembler2/trunk/debian/copyright
trunk/packages/mapsembler2/trunk/debian/docs
trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
trunk/packages/mapsembler2/trunk/debian/patches/series
trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
trunk/packages/mapsembler2/trunk/debian/rules
Log:
add patch for debian hardening, update copyright
Modified: trunk/packages/mapsembler2/trunk/debian/copyright
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/copyright 2014-08-18 16:58:25 UTC
(rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/copyright 2014-08-18 17:11:41 UTC
(rev 17770)
@@ -6,6 +6,7 @@
results_visualization
mapsembler2_extremities/thirdparty/gatb-core/thirdparty/boost
mapsembler2_extremities/thirdparty/gatb-core/thirdparty/hdf5
+ mapsembler2_extremities/thirdparty/gatb-core/doc/design
Files: mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/*
Copyright: 2013 Giuseppe Ottaviano <[email protected]>
@@ -55,8 +56,26 @@
Files: minia/*
Copyright: 2012 Rayan Chiki <[email protected]>
2012 Guillaume Rizk
-License: CeCILL
+License: AGPL-3+
+Files: mapsembler2_extremities/thirdparty/gatb-core/*
+Copyright: 2014 INRIA R.Chikhi, G.Rizk, E.Drezen
+Licence: AGPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ The complete text of the GNU Affero General Public License
+ can be found in the file `/usr/share/doc/mapsembler2/LICENCE.md.gz'.
+
Files: *
Copyright: 2013 INRIA / IRISA
License: AGPL-3+
Modified: trunk/packages/mapsembler2/trunk/debian/docs
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/docs 2014-08-18 16:58:25 UTC
(rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/docs 2014-08-18 17:11:41 UTC
(rev 17770)
@@ -1 +0,0 @@
-LICENCE.md
Modified: trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/mapsembler2.manpages
2014-08-18 17:11:41 UTC (rev 17770)
@@ -1,5 +1,5 @@
mapsembler2_extremities.1
-mapsembler2_extend.1
+mapsembler_extend.1
kissreads.1
kissreads_graph.1
Added: trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
(rev 0)
+++ trunk/packages/mapsembler2/trunk/debian/patches/add_hardening
2014-08-18 17:11:41 UTC (rev 17770)
@@ -0,0 +1,67 @@
+Index: mapsembler2_pipeline/kissreads/Makefile
+===================================================================
+--- mapsembler2_pipeline.orig/kissreads/Makefile
++++ mapsembler2_pipeline/kissreads/Makefile
+@@ -20,11 +20,15 @@ CC =gcc
+ # optimized flags
+
+ #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!ยง
+-CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
++#CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
+ CFLAGS+=$(MYFLAGS)
+ #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+ LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+
++CPPFLAGS += $(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS)
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
++
+ ## debug flags
+
+
+Index: mapsembler2_pipeline/kissreads_graph/makefile
+===================================================================
+--- mapsembler2_pipeline.orig/kissreads_graph/makefile
++++ mapsembler2_pipeline/kissreads_graph/makefile
+@@ -4,6 +4,9 @@ EXEC=kissreads_graph
+ #Loader.cpp CFLAGS= -g -lz -std=c++11 -DMINIA_IS_IN_PARENT_FOLDER
+ #Loader.cpp
+ CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz
-DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+ #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ SRC=block_allocator.cpp DeBruijnGraph.cpp Fragment.cpp json.cpp
read_coherence_mapsembler/libchash.cpp read_coherence_mapsembler/couple.cpp
read_coherence_mapsembler/misc_tools.cpp
read_coherence_mapsembler/read_groups.cpp
read_coherence_mapsembler/consensus_common.cpp
read_coherence_mapsembler/list.cpp
read_coherence_mapsembler/read_coherence.cpp
read_coherence_mapsembler/interface_libchash.cpp commons.cpp ../minia/Kmer.cpp
../minia/Bank.cpp Loader.cpp ReadMapper.cpp
+ OBJ= $(SRC:.cpp=.o)
+@@ -48,7 +51,7 @@ endif
+ all: $(EXEC)
+
+ kissreads_graph: $(OBJ) KissReadsGraph.cpp
+- $(CC) -o $@ $^ $(CFLAGS)
++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+
+ %.o: %.cpp %.h
+ $(CC) -lz -o $@ -c $< $(CFLAGS)
+Index: mapsembler2_pipeline/mapsembler2_extend/makefile
+===================================================================
+--- mapsembler2_pipeline.orig/mapsembler2_extend/makefile
++++ mapsembler2_pipeline/mapsembler2_extend/makefile
+@@ -3,6 +3,9 @@ EXEC=mapsembler_extend
+ #CFLAGS= -O4 -lz --std=gnu++0x
+ #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ CFLAGS= -O3 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS += $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -lz
-DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+ #CFLAGS= -g -lz --std=gnu++0x -DMINIA_IS_IN_PARENT_FOLDER
+ #CFLAGS= -g -lz -DMINIA_IS_IN_PARENT_FOLDER
+ SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp
../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp
../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp
../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp
../minia/OAHash.cpp commons.cpp IterativeExtensions.cpp Fragment_Bank.cpp
Fragment.cpp GraphOutput.cpp
+@@ -49,7 +52,7 @@ all: $(EXEC)
+
+ mapsembler_extend: $(OBJ) $(OBJ2) mapsembler_extend.cpp
+ #mapsembler: $(OBJ) $(OBJ2) test.cpp
+- $(CC) -o $@ $^ $(CFLAGS)
++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+
+ %.o: %.cpp %.h
+ $(CC) -lz -o $@ -c $< $(CFLAGS)
Modified: trunk/packages/mapsembler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/series 2014-08-18
16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/patches/series 2014-08-18
17:11:41 UTC (rev 17770)
@@ -1 +1,2 @@
use_debian_libs
+add_hardening
Modified: trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
2014-08-18 16:58:25 UTC (rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/patches/use_debian_libs
2014-08-18 17:11:41 UTC (rev 17770)
@@ -1,3 +1,8 @@
+Subject: use HDF5 lib in Debian
+Description: use Debian libs instead of embedded one
+Author: Olivier Sallou <[email protected]>
+Last-Updated: 2014-08-18
+Forwarded: no
Index:
mapsembler2_pipeline/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
===================================================================
---
mapsembler2_pipeline.orig/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/CMakeLists.txt
Modified: trunk/packages/mapsembler2/trunk/debian/rules
===================================================================
--- trunk/packages/mapsembler2/trunk/debian/rules 2014-08-18 16:58:25 UTC
(rev 17769)
+++ trunk/packages/mapsembler2/trunk/debian/rules 2014-08-18 17:11:41 UTC
(rev 17770)
@@ -26,14 +26,14 @@
cd kissreads && make clean
rm -f mapsembler2_extremities.1
- rm -f mapsembler2_extend.1
+ rm -f mapsembler_extend.1
rm -f kissreads.1
rm -f kissreads_graph.1
dh_clean
override_dh_install:
help2man --help-option=-h --no-discard-stderr
--version-string=$(SRC_VERSION)
./mapsembler2_extremities/build/mapsembler2_extremities >
mapsembler2_extremities.1
- help2man --help-option=-h --no-discard-stderr
--version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend >
mapsembler2_extend.1
+ help2man --help-option=-h --no-discard-stderr
--version-string=$(SRC_VERSION) ./mapsembler2_extend/mapsembler_extend >
mapsembler_extend.1
help2man --help-option=-h --no-discard-stderr
--version-string=$(SRC_VERSION) ./kissreads/kissreads > kissreads.1
help2man --help-option=-h --no-discard-stderr
--version-string=$(SRC_VERSION) ./kissreads_graph/kissreads_graph >
kissreads_graph.1
dh_install
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