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	<title><![CDATA[BOL: How to install LoRDEC?]]></title>
	<link>https://bioinformaticsonline.com/answers/view/39398/how-to-install-lordec?</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/answers/view/39398/how-to-install-lordec</guid>
	<pubDate>Sat, 25 May 2019 13:15:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/answers/view/39398/how-to-install-lordec</link>
	<title><![CDATA[How to install LoRDEC?]]></title>
	<description><![CDATA[<p>Hi!</p><p>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 .</p><p>Please see the make file of tool.</p><p># external resources<br />GATB_VER=1.1.0<br />GATB=gatb-core-$(GATB_VER)-Linux<br /><br /># FLAGS<br />CPPFLAGS =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -I$(GATB)/include/ -std=c++0x -O2 # -g # -O3 -DOLD_GATB # put pre-processor settings (-I, -D, etc) here<br />CXXFLAGS =gcc-5.4.0<br />&nbsp;#-Wall&nbsp; # put compiler settings here<br /># put linker settings here<br />LDFLAGS =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -L$(GATB)/lib/ -lgatbcore -lhdf5 -ldl -lz -lpthread -std=c++0x<br />#CXX&nbsp;&nbsp; &nbsp;= g++ # $(CXXFLAGS)<br />RM &nbsp;&nbsp;&nbsp; &nbsp;= rm -f <br />MV&nbsp;&nbsp; &nbsp;= mv<br /><br />CFILES_CORRECT = lordec-correct.cpp<br />CFILES_STATS = lordec-stat.cpp<br />CFILES_TRIM = lordec-trim.cpp<br />CFILES_TRIM_SPLIT = lordec-trim-split.cpp<br />CFILES_GRAPH = lordec-build-SR-graph.cpp<br /><br />OBJS_CORRECT&nbsp;&nbsp; &nbsp;= $(CFILES_CORRECT:.cpp=.o)<br />OBJS_STATS&nbsp;&nbsp; &nbsp;= $(CFILES_STATS:.cpp=.o)<br />OBJS_TRIM&nbsp;&nbsp; &nbsp;= $(CFILES_TRIM:.cpp=.o)<br />OBJS_TRIM_SPLIT&nbsp;&nbsp; &nbsp;= $(CFILES_TRIM_SPLIT:.cpp=.o)<br /><br />PROG&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;= LoRDEC<br />PROG_CORRECT&nbsp;&nbsp; &nbsp;= lordec-correct<br />PROG_STATS&nbsp;&nbsp; &nbsp;= lordec-stat<br />PROG_TRIM&nbsp;&nbsp; &nbsp;= lordec-trim<br />PROG_TRIM_SPLIT&nbsp;&nbsp; &nbsp;= lordec-trim-split<br />PROG_GRAPH&nbsp;&nbsp; &nbsp;= lordec-build-SR-graph<br /><br /># History of versions<br />VERSION=0.4.1<br />VERSION=0.5<br /><br />LICENSE=../LICENSE/Licence_CeCILL_V2.1-en.txt<br /><br /># for testing<br />DATA=./DATA<br />RES=./RES<br />TEST_SCRIPT=test-lordec.sh<br /><br /># These also need to be included in distribution package<br />HPPFILES=lordec-gen.hpp<br /><br />all:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)<br /><br />$(PROG_CORRECT):&nbsp;&nbsp; &nbsp;$(OBJS_CORRECT)<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $(OBJS_CORRECT) $(LDFLAGS) -o $@<br /><br />$(PROG_STATS):&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(OBJS_STATS)<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $(OBJS_STATS) $(LDFLAGS) -o $@ <br /><br />$(PROG_TRIM):&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(OBJS_TRIM)<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $(OBJS_TRIM) $(LDFLAGS) -o $@ <br /><br />$(PROG_TRIM_SPLIT):&nbsp;&nbsp; &nbsp;$(OBJS_TRIM_SPLIT)<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $(OBJS_TRIM_SPLIT) $(LDFLAGS) -o $@ <br /><br />$(PROG_GRAPH):&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CFILES_GRAPH)<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX)&nbsp; $@.cpp -o $@ $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS)<br /><br /><br />$(OBJS_CORRECT):&nbsp;&nbsp; &nbsp;%.o: %.cpp<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $&lt; $(CPPFLAGS) -c<br /><br />$(OBJS_STATS):&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;%.o: %.cpp<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $&lt; $(CPPFLAGS) -c <br /><br />$(OBJS_TRIM):&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;%.o: %.cpp<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $&lt; $(CPPFLAGS) -c <br /><br />$(OBJS_TRIM_SPLIT):&nbsp;&nbsp; &nbsp;%.o: %.cpp<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(CXX) $&lt; $(CPPFLAGS) -c <br /><br />install_dep:<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;wget http://gatb-core.gforge.inria.fr/versions/bin/gatb-core-$(GATB_VER)-Linux.tar.gz &amp;&amp; \<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;tar -axf gatb-core-$(GATB_VER)-Linux.tar.gz<br /><br />bin:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;mkdir bin<br /><br />instbin:<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(MV) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH) bin<br /><br />clean:<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(RM) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT) $(RES)/*<br /><br />purge:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;clean<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;$(RM) $(PROG_CORRECT) $(PROG_STATS) $(PROG_TRIM) $(PROG_TRIM_SPLIT) $(PROG_GRAPH)<br /><br />test:&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;<br />&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;./$(TEST_SCRIPT)</p>]]></description>
	<dc:creator>Nadia Baig</dc:creator>
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