From 32dca7baf7a24666dad5cf0142eb0b5e985a5b5f Mon Sep 17 00:00:00 2001 From: Karolis Ramanauskas Date: Sat, 22 Feb 2020 21:48:54 -0600 Subject: [PATCH 1/3] jellyfish-2.2.4 -> jellyfish-2.3.0. --- Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index b9a7f7d..dfa6019 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ CXX = g++ CXXFLAGS= -Wall -O3 -std=c++0x -LINKFLAGS = -I . -lpthread -lz +LINKFLAGS = -I . -lpthread -lz DEBUG= jellyfishPath = `which jellyfish` jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'` @@ -11,13 +11,13 @@ all: main.o $(OBJECTS) then \ 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 ;\ + wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz ;\ tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\ 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: From 15461be2114c25f42c3eea6f3bff977f7e11bd7a Mon Sep 17 00:00:00 2001 From: Karolis Ramanauskas Date: Sat, 22 Feb 2020 21:52:40 -0600 Subject: [PATCH 2/3] Fix changes in the previous commit. jellyfish-2.2.4 -> jellyfish-2.3.0. --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index dfa6019..d15f0c4 100644 --- a/Makefile +++ b/Makefile @@ -12,7 +12,7 @@ all: main.o $(OBJECTS) if [ ! -f ./jellyfish/bin/jellyfish ] ; \ then \ wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz ;\ - tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\ + tar -xzf jellyfish.tar.gz ; mv jellyfish-2.3.0 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\ fi;\ fi ; From 571d204dc69b05b40729eded7755920fd5677be1 Mon Sep 17 00:00:00 2001 From: Karolis Ramanauskas Date: Mon, 10 Aug 2020 04:41:05 -0500 Subject: [PATCH 3/3] Makefile edits: try 'curl' if 'wget' fails. macOS does not include 'wget' by default. --- Makefile | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/Makefile b/Makefile index d15f0c4..53e8128 100644 --- a/Makefile +++ b/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/v2.3.0/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 ErrorCorrection.o: ErrorCorrection.cpp ErrorCorrection.h clean: - rm *.o *.gch rcorrector + rm -rf *.o *.gch rcorrector jellyfish