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--- Makefile.ori 2018-04-21 17:47:38.017147315 +0200
+++ Makefile 2018-04-21 17:48:29.038679685 +0200
@@ -2,14 +2,14 @@
CXXFLAGS= -O2 -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -std=c++0x
LINKFLAGS = -I . -lpthread -lz
DEBUG=
-jellyfishPath = `which jellyfish`
-jellyfishVersion = `jellyfish --version | cut -f2 -d' ' | cut -f1 -d'.'`
+jellyfishPath = `which jellyfish2`
+jellyfishVersion = `jellyfish2 --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) ] || [ $(jellyfishVersion) -ne 2 ] ; \
then \
- if [ ! -f ./jellyfish/bin/jellyfish ] ; \
+ if [ ! -f ./jellyfish/bin/jellyfish2 ] ; \
then \
wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.2.4/jellyfish-2.2.4.tar.gz ;\
tar -xzf jellyfish.tar.gz ; mv jellyfish-2.2.4 jellyfish ; rm jellyfish.tar.gz ; cd jellyfish && ./configure && make ;\
--- run_rcorrector.pl.ori 2018-04-21 17:48:43.459112787 +0200
+++ run_rcorrector.pl 2018-04-21 17:49:18.070152287 +0200
@@ -42,10 +42,10 @@
die "$usage\n" ;
}
-my $jellyfishBin = "jellyfish" ;
-if ( -e "$WD/jellyfish/bin/jellyfish" )
+my $jellyfishBin = "jellyfish2" ;
+if ( -e "$WD/jellyfish/bin/jellyfish2" )
{
- $jellyfishBin = "$WD/jellyfish/bin/jellyfish" ;
+ $jellyfishBin = "$WD/jellyfish/bin/jellyfish2" ;
}
my $fileArguments ;
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