--- trinity-plugins/Makefile	2016-12-25 12:01:25.000000000 +0200
+++ trinity-plugins/Makefile	2016-12-25 12:08:47.000000000 +0200
@@ -22,26 +22,12 @@
 
 
 
-trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
-
-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
+trinity_essentials:  scaffold_iworm_contigs_target fastool_target parafly_target
 
 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)
@@ -52,7 +38,7 @@
 
 
 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