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
|
Description: use Debian packages dependencies for extension build
Author: Sascha Steinbiss <satta@debian.org>
--- a/setup.py
+++ b/setup.py
@@ -4,47 +4,46 @@
import glob
from setuptools import setup, find_packages, Extension
-minimap_c_files = [
- 'bseq.c',
- 'index.c',
- 'kthread.c',
- 'map.c',
- 'misc.c',
- 'sdust.c',
- 'sketch.c',
-]
-
-minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
-minimap_c_files.append(os.path.join('ariba', 'ext', 'minimap_ariba.cpp'))
+#minimap_c_files = [
+# 'bseq.c',
+# 'index.c',
+# 'kthread.c',
+# 'map.c',
+# 'misc.c',
+# 'sdust.c',
+# 'sketch.c',
+#]
+#minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
+minimap_c_files = [os.path.join('ariba', 'ext', 'minimap_ariba.cpp')]
minimap_mod = Extension(
"minimap_ariba",
minimap_c_files,
- extra_link_args=['-lz'],
- include_dirs=[os.path.join('third_party', 'minimap-0.2')],
+ extra_link_args=['-lz', '-lminimap'],
+ include_dirs=[os.path.join(os.path.sep, 'usr', 'include', 'minimap')],
)
-fermilite_c_files = [
- 'bfc.c',
- 'bseq.c',
- 'bubble.c',
- 'htab.c',
- 'ksw.c',
- 'kthread.c',
- 'mag.c',
- 'misc.c',
- 'mrope.c',
- 'rld0.c',
- 'rle.c',
- 'rope.c',
- 'unitig.c'
-]
-fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
-fermilite_c_files.append(os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp'))
+#fermilite_c_files = [
+# 'bfc.c',
+# 'bseq.c',
+# 'bubble.c',
+# 'htab.c',
+# 'ksw.c',
+# 'kthread.c',
+# 'mag.c',
+# 'misc.c',
+# 'mrope.c',
+# 'rld0.c',
+# 'rle.c',
+# 'rope.c',
+# 'unitig.c'
+#]
+#fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
+fermilite_c_files = [os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp')]
fermilite_mod = Extension(
"fermilite_ariba",
fermilite_c_files,
- extra_link_args=['-lz'],
- include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
+ extra_link_args=['-lz', '-lfml'],
+ #include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
)
vcfcall_mod = Extension(
|
