From 412c1a2821c5a4cbe2e68e4e9f4e2026a86d25f7 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Sat, 7 Jun 2014 19:45:27 -0500
Subject: [PATCH] Renamed makefile as Makefile

---
 EBSeq/{makefile => Makefile} | 2 ++
 makefile => Makefile         | 4 ++--
 2 files changed, 4 insertions(+), 2 deletions(-)
 rename EBSeq/{makefile => Makefile} (91%)
 rename makefile => Makefile (99%)

diff --git a/EBSeq/makefile b/EBSeq/Makefile
similarity index 91%
rename from EBSeq/makefile
rename to EBSeq/Makefile
index 898c8fa..78b6d60 100644
--- a/EBSeq/makefile
+++ b/EBSeq/Makefile
@@ -1,6 +1,8 @@
 CC = g++
 PROGRAMS = EBSeq rsem-for-ebseq-calculate-clustering-info
 
+.PHONY : all EBSeq clean
+
 all : $(PROGRAMS)
 
 EBSeq : 
diff --git a/makefile b/Makefile
similarity index 99%
rename from makefile
rename to Makefile
index 76e1ac3..a9a705f 100644
--- a/makefile
+++ b/Makefile
@@ -3,6 +3,8 @@ CFLAGS = -Wall -c -I.
 COFLAGS = -Wall -O3 -ffast-math -c -I.
 PROGRAMS = rsem-extract-reference-transcripts rsem-synthesis-reference-transcripts rsem-preref rsem-parse-alignments rsem-build-read-index rsem-run-em rsem-tbam2gbam rsem-run-gibbs rsem-calculate-credibility-intervals rsem-simulate-reads rsem-bam2wig rsem-get-unique rsem-bam2readdepth rsem-sam-validator rsem-scan-for-paired-end-reads
 
+.PHONY : all ebseq clean
+
 all : $(PROGRAMS)
 
 sam/libbam.a :
@@ -137,8 +139,6 @@ rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam
 rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a
 	$(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@
 
-.PHONY: ebseq
-
 ebseq :
 	cd EBSeq ; ${MAKE} all
 
-- 
2.39.2