[mmseq/el5] Reinstate boost141 flag fixes for el5 branch

[verdurin]

commit 16d9e27ba7ff13a6b0d1d1eea06b3dda5ed533d9
Author: Adam Huffman <bloch at verdurin.com>
Date:   Fri Oct 7 17:24:51 2011 +0100

    Reinstate boost141 flag fixes for el5 branch

 mmseq-flags.patch |   19 ++++++++++++++++---
 1 files changed, 16 insertions(+), 3 deletions(-)
---
diff --git a/mmseq-flags.patch b/mmseq-flags.patch
index b3c361c..130bb3b 100644
--- a/mmseq-flags.patch
+++ b/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