blob: 604f657d4c42940f24b81187f7d82ed0bb128607 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
|
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)
|
GitWeb