From f428a0be52a2d112d653d1945562e2bdecd137d6 Mon Sep 17 00:00:00 2001
From: Nathan Weeks <weeks@iastate.edu>
Date: Sun, 11 Nov 2012 20:55:27 -0600
Subject: [PATCH] Specify libraries after the object files that reference them
 for portability. Now compiles on Ubuntu 12.04 LTS with the default gcc 4.6.3
 compiler.

Fix path to test source files so "make test" works.
---
 Makefile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index b39dc1c..5116a4b 100644
--- a/Makefile
+++ b/Makefile
@@ -21,13 +21,13 @@ util.o: $(SDIR)/util.c $(SDIR)/kseq.h $(SDIR)/scythe.h
 prob.o: $(SDIR)/prob.c $(SDIR)/scythe.h
 	$(CC) $(CFLAGS) -c $(SDIR)/$*.c
 tests.o: $(SDIR)/tests/tests.c $(SDIR)/scythe.h
-	$(CC) $(CFLAGS) -c $(SDIR)/$*.c
+	$(CC) $(CFLAGS) -c $(SDIR)/tests/$*.c
 
 valgrind: build
 	valgrind --leak-check=full --show-reachable=yes ./scythe -a solexa_adapters.fa test.fastq
 
 test: match.o util.o prob.o tests.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $? -o tests && ./tests
+	$(CC) $(CFLAGS) $? -o tests $(LDFLAGS) && ./tests 
 
 testclean:
 	rm -rf ./tests
@@ -42,7 +42,7 @@ dist:
 	tar -zcf $(ARCHIVE).tar.gz src Makefile
 
 build: match.o scythe.o util.o prob.o 
-	$(CC) $(CFLAGS) $(LDFLAGS) $? -o scythe
+	$(CC) $(CFLAGS) $? -o scythe $(LDFLAGS) 
 
 debug:
-	$(CC) $(LDFLAGS) $(DEBUG) -o scythe src/*.c
\ No newline at end of file
+	$(CC) $(DEBUG) -o scythe src/*.c $(LDFLAGS)