<commit_before>PATH := bin:util/mafft/bin:util/tcoffee/compile:util/standard-RAxML:util/anaconda_ete/bin:util/OBITools/bin:$(PATH)

.PHONY: all clean dependencies obitools

all:
	@echo "MetBaN itself doesn't require building. Use"
	@echo "make dependencies # to auto-install required tools in ./util/"
	@echo "make sure that Python-dev packages are installed"

clean:
	-rm -fr util

dependencies:
	hash mafft || $(MAKE) util/mafft
	hash t_coffee || $(MAKE) util/tcoffee
	hash raxmlHPC || $(MAKE) util/raxml
	hash conda ete3 || $(MAKE) util/miniconda
	#hash vcfutils.pl || $(MAKE) util/bcftools
	hash obigrep || $(MAKE) util/obitools

obitools:
	hash obigrep || $(MAKE) util/only_obitools

util/mafft:
	mkdir -p util
	cd util && wget http://mafft.cbrc.jp/alignment/software/mafft-7.310-with-extensions-src.tgz 
	cd util && tar xfvz mafft-*-with-extensions-src.tgz && rm mafft-*-with-extensions-src.tgz && mv mafft-*-with-extensions mafft
	cd util/mafft && mkdir -p bin && sed -i -e 's?PREFIX = \/usr\/local?PREFIX = '`pwd`'?' core/Makefile
	cd util/mafft && sed -i -e 's?PREFIX = \/usr\/local?PREFIX = '`pwd`'?' extensions/Makefile
	cd util/mafft/core && make clean && make && make install

util/tcoffee:
	mkdir -p util
	cd util && git clone https://github.com/cbcrg/tcoffee.git
	cd util/tcoffee/compile && make t_coffee

util/raxml:
	mkdir -p util
	cd util && git clone https://github.com/stamatak/standard-RAxML.git
	cd util/standard-RAxML && make -f Makefile.gcc && make -f Makefile.PTHREADS.gcc
	cd util/standard-RAxML && make -f Makefile.AVX2.gcc && make -f Makefile.AVX2.PTHREADS.gcc
	cd util/standard-RAxML && make -f Makefile.AVX.gcc && make -f Makefile.AVX.PTHREADS.gcc<commit_msg>fixed legacy raxml<commit_after>PATH := bin:util/mafft/bin:util/tcoffee/compile:util/standard-RAxML:util/anaconda_ete/bin:util/OBITools/bin:$(PATH)

.PHONY: all clean dependencies obitools

all:
	@echo "MetBaN itself doesn't require building. Use"
	@echo "make dependencies # to auto-install required tools in ./util/"
	@echo "make sure that Python-dev packages are installed"

clean:
	-rm -fr util

dependencies:
	hash mafft || $(MAKE) util/mafft
	hash t_coffee || $(MAKE) util/tcoffee
	hash raxmlHPC-PTHREADS || $(MAKE) util/raxml
	hash conda ete3 || $(MAKE) util/miniconda
	#hash vcfutils.pl || $(MAKE) util/bcftools
	hash obigrep || $(MAKE) util/obitools

obitools:
	hash obigrep || $(MAKE) util/only_obitools

util/mafft:
	mkdir -p util
	cd util && wget http://mafft.cbrc.jp/alignment/software/mafft-7.310-with-extensions-src.tgz 
	cd util && tar xfvz mafft-*-with-extensions-src.tgz && rm mafft-*-with-extensions-src.tgz && mv mafft-*-with-extensions mafft
	cd util/mafft && mkdir -p bin && sed -i -e 's?PREFIX = \/usr\/local?PREFIX = '`pwd`'?' core/Makefile
	cd util/mafft && sed -i -e 's?PREFIX = \/usr\/local?PREFIX = '`pwd`'?' extensions/Makefile
	cd util/mafft/core && make clean && make && make install

util/tcoffee:
	mkdir -p util
	cd util && git clone https://github.com/cbcrg/tcoffee.git
	cd util/tcoffee/compile && make t_coffee

util/raxml:
	mkdir -p util
	cd util && git clone https://github.com/stamatak/standard-RAxML.git
	cd util/standard-RAxML && make -f Makefile.gcc && make -f Makefile.PTHREADS.gcc
	cd util/standard-RAxML && make -f Makefile.AVX2.gcc && make -f Makefile.AVX2.PTHREADS.gcc
	cd util/standard-RAxML && make -f Makefile.AVX.gcc && make -f Makefile.AVX.PTHREADS.gcc
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