Merge branch 'master' into el5

Conflicts:
	mmseq-flags.patch

mmseq-flags.patch

@@ -1,6 +1,15 @@
 --- mmseq_0.9.14/Makefile	2011-09-20 11:27:55.000000000 +0100
-+++ mmseq_0.9.14.new/Makefile	2011-10-07 16:13:01.261226334 +0100
-@@ -35,7 +35,7 @@
++++ mmseq_0.9.14.new/Makefile	2011-10-07 17:24:00.961086740 +0100
+@@ -26,7 +26,7 @@
+ .PHONY : all
+ 
+ mmseq : sokal.o mmseq.cpp
+-	$(CXX) ${MACROS} $(CXXFLAGS) -fopenmp -O3 sokal.o mmseq.cpp -o mmseq ${LIBS}
++	$(CXX) ${MACROS} $(CXXFLAGS) -I/usr/include/boost141 -fopenmp -O3 sokal.o mmseq.cpp -o mmseq ${LIBS} -L/usr/lib64/boost141 -L/usr/lib/boost141
+ 
+ static: sokal.o mmseq.cpp
+ 	$(CXX) ${MACROS} ${STATICFLAG} -fopenmp -O3 sokal.o mmseq.cpp -o ${STATICBIN} ${STATICLIBS}
+@@ -35,10 +35,10 @@
  	$(CXX) $(CXXFLAGS) -c sokal.cc
  
  fasta.o : fasta.c fasta.h
@@ -8,4 +17,8 @@
 +	$(CC) $(CXXFLAGS) -c fasta.c
  
  bam2hits : fasta.o bam2hits.cpp
- 	${CXX} ${MACROS} $(CXXFLAGS) -fopenmp -O3 fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H}
+-	${CXX} ${MACROS} $(CXXFLAGS) -fopenmp -O3 fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H}
++	${CXX} ${MACROS} $(CXXFLAGS) -I/usr/include/boost141 -fopenmp -O3 fasta.o bam2hits.cpp -o bam2hits ${LIBS_B2H} -L/usr/lib64/boost141 -L/usr/lib/boost141
+ 
+ hpc : mmseq_hpc bam2hits_hpc
+ .PHONY : all

mmseq.spec

@@ -12,7 +12,7 @@ Patch0:		mmseq-sam-header.patch
 Patch2:		mmseq-zlib.patch
 BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
-BuildRequires:	boost-devel
+BuildRequires:	boost141-devel
 BuildRequires:	samtools-devel
 BuildRequires:	gsl-devel
 BuildRequires:	zlib-devel
@@ -86,8 +86,8 @@ rm -rf %{buildroot}
 * Wed Aug 17 2011 Adam Huffman <bloch@verdurin.com> - 0.9.12-1
 - upstream release 0.9.12 fixing a possible segfault
 
-* Thu Jul 21 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-2
-- rebuild for new Boost in Rawhide
+* Fri Jun 17 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-1
+- use boost141 on EPEL5
 
 * Sat May 28 2011 Adam Huffman <bloch@verdurin.com> - 0.9.11-1
 - new upstream release