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Question: Question: How to install LoRDEC?

Nadia Baig
2041 days ago

Question: How to install LoRDEC?

Hi!

I want to install LoRDEC using the following tutorial (https://biosphere.france-bioinformatique.fr/wikia2/index.php/Lordec. I am not able to install it in my linux system. Actually the 4th point of this installation tutorial is quite confusing. I am not able to change the variables in make file .

Please see the make file of tool.

# external resources
GATB_VER=1.1.0
GATB=gatb-core-$(GATB_VER)-Linux

# FLAGS
CPPFLAGS =        -I$(GATB)/include/ -std=c++0x -O2 # -g # -O3 -DOLD_GATB # put pre-processor settings (-I, -D, etc) here
CXXFLAGS =gcc-5.4.0
 #-Wall  # put compiler settings here
# put linker settings here
LDFLAGS =         -L$(GATB)/lib/ -lgatbcore -lhdf5 -ldl -lz -lpthread -std=c++0x
#CXX    = g++ # $(CXXFLAGS)
RM      = rm -f
MV    = mv

CFILES_CORRECT = lordec-correct.cpp
CFILES_STATS = lordec-stat.cpp
CFILES_TRIM = lordec-trim.cpp
CFILES_TRIM_SPLIT = lordec-trim-split.cpp
CFILES_GRAPH = lordec-build-SR-graph.cpp

OBJS_CORRECT    = $(CFILES_CORRECT:.cpp=.o)
OBJS_STATS    = $(CFILES_STATS:.cpp=.o)
OBJS_TRIM    = $(CFILES_TRIM:.cpp=.o)
OBJS_TRIM_SPLIT    = $(CFILES_TRIM_SPLIT:.cpp=.o)

PROG        = LoRDEC
PROG_CORRECT    = lordec-correct
PROG_STATS    = lordec-stat
PROG_TRIM    = lordec-trim
PROG_TRIM_SPLIT    = lordec-trim-split
PROG_GRAPH    = lordec-build-SR-graph

# History of versions
VERSION=0.4.1
VERSION=0.5

LICENSE=../LICENSE/Licence_CeCILL_V2.1-en.txt

# for testing
DATA=./DATA
RES=./RES
TEST_SCRIPT=test-lordec.sh

# These also need to be included in distribution package
HPPFILES=lordec-gen.hpp

all:        $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)

$(PROG_CORRECT):    $(OBJS_CORRECT)
            $(CXX) $(OBJS_CORRECT) $(LDFLAGS) -o $@

$(PROG_STATS):        $(OBJS_STATS)
            $(CXX) $(OBJS_STATS) $(LDFLAGS) -o $@

$(PROG_TRIM):        $(OBJS_TRIM)
            $(CXX) $(OBJS_TRIM) $(LDFLAGS) -o $@

$(PROG_TRIM_SPLIT):    $(OBJS_TRIM_SPLIT)
            $(CXX) $(OBJS_TRIM_SPLIT) $(LDFLAGS) -o $@

$(PROG_GRAPH):        $(CFILES_GRAPH)
            $(CXX)  $@.cpp -o $@ $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS)


$(OBJS_CORRECT):    %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_STATS):        %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_TRIM):        %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

$(OBJS_TRIM_SPLIT):    %.o: %.cpp
            $(CXX) $< $(CPPFLAGS) -c

install_dep:
        wget http://gatb-core.gforge.inria.fr/versions/bin/gatb-core-$(GATB_VER)-Linux.tar.gz && \
        tar -axf gatb-core-$(GATB_VER)-Linux.tar.gz

bin:        
        mkdir bin

instbin:
        $(MV) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH) bin

clean:
        $(RM) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT) $(RES)/*

purge:        clean
        $(RM) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)

test:        
        ./$(TEST_SCRIPT)

getting this error while compiling using make command.

++ lordec-correct.cpp -Igatb-core-1.1.0-Linux/include/ -std=c++0x -O2  -c
lordec-correct.cpp:43:40: fatal error: boost/graph/graph_traits.hpp: No such file or directory
compilation terminated.
Makefile:67: recipe for target 'lordec-correct.o' failed
make: *** [lordec-correct.o] Error 1

Nadia Baig 2041 days ago

Answers
0

You might need to install libboost (I presume you are using Ubuntu)

sudo apt-get install libboost-dev

its not working. actually first few lines of this make file needs to be changed. I am not able to figure out that part.

Nadia Baig 2040 days ago

0

It is certainly off topic, but HALC is the best choice for correction of long PacBio reads, when both, read size and quality, are the main focus of the analysis.

Lordec is not very useful and surprisingly hectic 

Ref: https://www.ncbi.nlm.nih.gov/pubmed/29268960/

0

Thanks neelam. To install HALC both BLASR and Lordec are needed.

0

Try HECIL, a new long read correction tool. https://github.com/NDBL/HECIL

thanks

Nadia Baig 2036 days ago