configure.ac    |  3 ++-
 src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
 2 files changed, 27 insertions(+), 26 deletions(-)

diff --git a/configure.ac b/configure.ac
index 75e9218..98b05d2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
 # set CFLAGS and CXXFLAGS
 #user_CFLAGS="${CXXFLAGS}"
 user_CFLAGS=${CFLAGS}
-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
+#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
+generic_CFLAGS=""
 ext_CFLAGS=""
 debug_CFLAGS=""
 user_LDFLAGS="$LDFLAGS"
diff --git a/src/Makefile.am b/src/Makefile.am
index dde692e..ebb9fcd 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -545,7 +545,7 @@ CLEANFILES = \
 	tophat2
 
 tophat2: tophat2.in
-	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
 
 #SUFFIXES = .py
 #.py:
@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
 #-- program sources
 
 prep_reads_SOURCES = prep_reads.cpp
-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) 
+prep_reads_LDADD = libtophat.a $(BAM_LIB)
+prep_reads_LDFLAGS = $(BAM_LDFLAGS) 
 
 segment_juncs_SOURCES = segment_juncs.cpp
-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
 
 long_spanning_reads_SOURCES = long_spanning_reads.cpp
-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
 
 gtf_juncs_SOURCES = gtf_juncs.cpp
-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
+gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
 
 juncs_db_SOURCES = juncs_db.cpp
-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+juncs_db_LDADD = libtophat.a $(BAM_LIB)
+juncs_db_LDFLAGS = $(BAM_LDFLAGS)
 
 tophat_reports_SOURCES = tophat_reports.cpp
-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
+tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
 
 fix_map_ordering_SOURCES = fix_map_ordering.cpp
-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
+fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
 
 bam2fastx_SOURCES = bam2fastx.cpp
-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+bam2fastx_LDADD = libgc.a $(BAM_LIB)
+bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
 
 bam_merge_SOURCES = bam_merge.cpp
-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
+bam_merge_LDFLAGS = $(BAM_LDFLAGS)
 
 sam_juncs_SOURCES = sam_juncs.cpp
-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+sam_juncs_LDADD = libtophat.a $(BAM_LIB)
+sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
 
 map2gtf_SOURCES = map2gtf.cpp
-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
+map2gtf_LDFLAGS = $(BAM_LDFLAGS)
 
 gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
+gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
+gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)