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
|
Author: Michael R. Crusoe <crusoe@debian.org>
Description: Use libhdf5-dev
Forwarded: not-needed
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,9 @@
CC=gcc
CFLAGS=-Wall -std=c++11 -g -fPIC -O3 $(FLAGS)
-LIBHDF5=./submods/hdf5/lib/libhdf5.a
-HDF5_LIB=-L./submods/hdf5/lib $(LIBHDF5)
-HDF5_INCLUDE=-I./submods/hdf5/include
+LIBHDF5=$(shell pkg-config --libs-only-L hdf5-serial | sed 's/^-L//')
+HDF5_LIB=$(shell pkg-config --libs hdf5-serial)
+HDF5_INCLUDE=$(shell pkg-config --cflags hdf5-serial)
LIBBWA=./submods/bwa/libbwa.a
BWA_LIB=-L./submods/bwa $(LIBBWA)
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@
"-f", "../../src/Makefile_bwa"
])
- if os.path.exists("./submods/hdf5/lib/libhdf5.a"):
+ if True: # os.path.exists("./submods/hdf5/lib/libhdf5.a"):
sys.stderr.write("Found libhdf5.a\n")
else:
@@ -101,7 +101,7 @@
include_dirs = [
"./submods",
- "./submods/hdf5/include",
+ subprocess.check_output("pkg-config --cflags hdf5-serial | sed 's/-I//'", shell=True, encoding='UTF-8').strip(),
"./submods/fast5/include",
"./submods/pdqsort",
"./submods/toml11",
@@ -109,14 +109,13 @@
],
library_dirs = [
- "./submods/bwa"
+ subprocess.check_output("pkg-config --libs-only-L hdf5-serial | sed 's/-L//'", shell=True, encoding='UTF-8').strip()
],
extra_objects = [
- "./submods/hdf5/lib/libhdf5.a"
],
- libraries = ["bwa", "z", "dl", "m"],
+ libraries = ["bwa", "hdf5", "z", "dl", "m"],
extra_compile_args = ["-std=c++11", "-O3"],
|
