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OS := $(shell uname)
COLLECTL_CODE="collectl-4.1.0"
PARAFLY_CODE="ParaFly-0.1.0"
TRIMMOMATIC_CODE=Trimmomatic-0.36
trinity_essentials: seqtk_target parafly_target trimmomatic_target
trimmomatic_target:
ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
seqtk_target:
tar xvf seqtk-trinity.v0.0.2.tar.gz
cd seqtk-trinity-0.0.2 && $(MAKE)
mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
parafly_target:
tar -zxvf ${PARAFLY_CODE}.tar.gz && \
cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` && $(MAKE) install && \
cp bin/ParaFly ../BIN/
##################################
### Needed for downstream analyses
##################################
plugins: slclust_target collectl_target
@echo "\n\n** Done building plugins **\n\n"
slclust_target:
cd slclust && $(MAKE) install
collectl_target:
cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl
clean:
rm -rf ./seqtk-trinity-0.0.2
cd scaffold_iworm_contigs && $(MAKE) clean
rm -f ./parafly # rm symlink
rm -f ./Trimmomatic # rm symlink
cd slclust && $(MAKE) clean
cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
@echo "\n\n** Done cleaning plugins area **"
###################################################################
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