--- trinity-plugins/Makefile	2016-07-01 23:32:24.478934797 +0400
+++ trinity-plugins/Makefile	2016-07-02 00:32:49.650063388 +0400
@@ -18,26 +18,27 @@
 
 
 
-trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
+#trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
+trinity_essentials:  scaffold_iworm_contigs_target fastool_target parafly_target
 
-trimmomatic_target:
-	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+#trimmomatic_target:
+#	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
 
 
-samtools:
-	tar xvf samtools-0.1.19.tar.bz2
-	cd samtools-0.1.19 && $(MAKE) ${LTINFO} 
-	mv samtools-0.1.19/samtools ./BIN/.
-
-jellyfish:
-	tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish
-	cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include"
-	mv tmp.jellyfish jellyfish
+#samtools:
+#	tar xvf samtools-0.1.19.tar.bz2
+#	cd samtools-0.1.19 && sed -i 's/$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread/$(CC) $(CPPFLAGS) -o $@ $^ -lz -lpthread /' Makefile && $(MAKE) ${LTINFO} 
+#	mv samtools-0.1.19/samtools ./BIN/.
+#
+#jellyfish:
+#	tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish
+#	cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include"
+#	mv tmp.jellyfish jellyfish
 
 htslib_target:
 #	tar xjvf htslib-1.2.1.tar.bz2
 #	cd htslib-1.2.1 && ./configure && $(MAKE)
-	tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
+	tar xvf ${HTSLIB_CODE} && sed -i 's/CPPFLAGS =/#CPPFLAGS =/' htslib/Makefile && cd htslib && $(MAKE)
 
 scaffold_iworm_contigs_target: htslib_target
 	cd scaffold_iworm_contigs && $(MAKE)
@@ -48,7 +49,7 @@
 
 
 parafly_target:
-	cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` && $(MAKE) install
+	cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CC=${PREFIX}/bin/gcc $(INCHWORM_CONFIGURE_FLAGS) CXX=${PREFIX}/bin/g++ CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install
 	ln -sf ${PARAFLY_CODE} parafly
 
 
