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|
OS := $(shell uname)
CXX = g++
CC = gcc
COLLECTL_CODE="collectl-4.1.0"
PARAFLY_CODE="ParaFly"
TRIMMOMATIC_CODE=Trimmomatic-0.36
trinity_essentials: seqtk_target parafly_target trimmomatic_target bamsifter_target
no_bamsifter: seqtk_target parafly_target trimmomatic_target
trimmomatic_target:
ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
seqtk_target:
cd seqtk-trinity && $(MAKE) CXX=$(CXX) CC=$(CC)
mv seqtk-trinity/seqtk-trinity ./BIN/.
parafly_target:
cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install && \
cp bin/ParaFly ../BIN/
bamsifter_target:
cd bamsifter && $(MAKE)
##################################
### Needed for downstream analyses
##################################
plugins: slclust_target collectl_target
@echo "\n\n** Done building plugins **\n\n"
slclust_target:
cd slclust && $(MAKE) CXX=$(CXX) CC=$(CC) install
collectl_target:
cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl
clean:
cd seqtk-trinity && $(MAKE) clean
cd scaffold_iworm_contigs && $(MAKE) clean
cd ${PARAFLY_CODE} && $(MAKE) clean
rm -f ./Trimmomatic # rm symlink
cd slclust && $(MAKE) clean
cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl
cd htslib && $(MAKE) clean
cd bamsifter && $(MAKE) clean
rm -f ./htslib.ok
@echo "\n\n** Done cleaning plugins area **"
###################################################################
|
