[med-svn] [tophat] 02/06: Fix Makefile for the embeded copy of samtools-0.1.18

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
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commit 924a11931c3bc2af10b42c35993d46c40ddc0964
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Mar 17 17:13:55 2016 +0100

    Fix Makefile for the embeded copy of samtools-0.1.18
---
 debian/patches/hardening4samtools.patch | 15 +++++++--------
 debian/patches/series                   |  2 +-
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/debian/patches/hardening4samtools.patch b/debian/patches/hardening4samtools.patch
index dc2142e..83d1570 100644
--- a/debian/patches/hardening4samtools.patch
+++ b/debian/patches/hardening4samtools.patch
@@ -1,22 +1,21 @@
-Description: add hardening flags to embedded copy of samtools
+Description: Don't overwrite CFLAGS, add CPPFLAGS and LDFLAGS fot the embedded
+copy of samtools
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
---- a/src/samtools-0.1.18/Makefile
-+++ b/src/samtools-0.1.18/Makefile
-@@ -1,5 +1,7 @@
+--- tophat.orig/src/samtools-0.1.18/Makefile
++++ tophat/src/samtools-0.1.18/Makefile
+@@ -1,5 +1,5 @@
  CC=			gcc
 -CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
-+CFLAGS=         $(shell dpkg-buildflags --get CFLAGS)
-+LDFLAGS=        $(shell dpkg-buildflags --get LDFLAGS)
 +
  DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
  KNETFILE_O=	knetfile.o
  LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -41,7 +43,7 @@ libbam.a:$(LOBJS)
+@@ -41,7 +41,7 @@
  		$(AR) -csru $@ $(LOBJS)
  
  samtools_0.1.18:lib-recur $(AOBJS)
 -		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz #$(LIBCURSES)
-+		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz $(LDFLAGS) #$(LIBCURSES) 
++		$(CC) $(CPPFLAGS) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf -lm -lz $(LDFLAGS) #$(LIBCURSES)
  
  razip:razip.o razf.o $(KNETFILE_O)
  		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
diff --git a/debian/patches/series b/debian/patches/series
index 0d4992a..7741a41 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
+hardening4samtools.patch
 remove_3rd_party_code.patch
 fix_includes_path.patch
-hardening4samtools.patch

-- 
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