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Author: Michael R. Crusoe <crusoe@debian.org>
Description: Use libhdf5-dev
Forwarded: not-needed
--- uncalled.orig/Makefile
+++ uncalled/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)
--- uncalled.orig/setup.py
+++ uncalled/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", #TODO: consistent incl paths?
- "./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",
@@ -110,7 +110,7 @@
library_dirs = [
"./submods/bwa",
- "./submods/hdf5/lib"
+ subprocess.check_output("pkg-config --libs-only-L hdf5-serial | sed 's/-L//'", shell=True, encoding='UTF-8').strip()
],
libraries = ["bwa", "hdf5", "z", "dl", "m"],
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