Merge pull request #25 from karolisr/master

Update Jellyfish to version 2.3.0

Makefile

@@ -1,24 +1,28 @@
-CXX = g++
-CXXFLAGS= -Wall -O3 -std=c++0x
-LINKFLAGS = -I . -lpthread -lz 
+CXX=g++
+CXXFLAGS=-Wall -O3 -std=c++0x
+LINKFLAGS=-I . -lpthread -lz
 DEBUG=
-jellyfishPath = `which jellyfish`
-jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'`
-OBJECTS = KmerCode.o ErrorCorrection.o
+jellyfishPath=`which jellyfish`
+jellyfishVersion=`jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'`
+OBJECTS=KmerCode.o ErrorCorrection.o
 all: main.o $(OBJECTS)
 	$(CXX) -o rcorrector $(CXXFLAGS) $(OBJECTS) main.o $(LINKFLAGS)
-	if [ ! $(jellyfishPath) ] || [ $(jellyfishVersion) -ne 2 ] ; \
+	if [ ! $(jellyfishPath) ] || [ $(jellyfishVersion) -ne 2 ] ;\
 	then \
-		if [ ! -f ./jellyfish/bin/jellyfish ] ; \
+		if [ ! -f ./jellyfish/bin/jellyfish ] ;\
 		then \
-			wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.2.4/jellyfish-2.2.4.tar.gz ;\
-			tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
+			wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz ;\
+			if [ ! -f jellyfish.tar.gz ] ;\
+			then \
+				curl -L -o jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz ;\
+			fi;\
+			tar -xzf jellyfish.tar.gz ; mv jellyfish-2.3.0 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
 		fi;\
-	fi ;
+	fi;
 
 main.o: main.cpp utils.h Reads.h Store.h File.h
-KmerCode.o: KmerCode.cpp KmerCode.h 
+KmerCode.o: KmerCode.cpp KmerCode.h
 ErrorCorrection.o: ErrorCorrection.cpp ErrorCorrection.h
 
 clean:
-	rm *.o *.gch rcorrector
+	rm -rf *.o *.gch rcorrector jellyfish