Makefile

.PHONY: clean all test publish

## Do not specify patch version
HYPHY_VERSION=2.5

TAG:=$(shell git describe --tags `git rev-list --tags --max-count=1` --match="$(HYPHY_VERSION)".*)

all: install

hyphy:
	echo "installing hyphy"
	@if ! test -d ./.hyphy; then git clone http://github.com/veg/hyphy.git ./.hyphy/; fi
	@cd ./.hyphy && git checkout $(TAG) && cmake -DNOAVX=ON . && make -j 4 hyphy && make -j 4 HYPHYMPI && cd ../

update-hyphy:
	echo "updating hyphy to latest release"
	@cd ./.hyphy && git pull origin master --tags && git checkout $(TAG) && cmake -DNOAVX=ON . && make -j 4 hyphy && make -j 4 HYPHYMPI && cd ../

hyphy-analyses:
	echo "installing hyphy-analyses"
	@if ! test -d ./.hyphy-analyses; then git clone http://github.com/veg/hyphy-analyses.git ./.hyphy-analyses/; fi
	
hivtrace:
	@mkdir -p ./.python
	@virtualenv ./.python/env/
	@./.python/env/bin/pip install numpy
	@./.python/env/bin/pip install biopython
	@./.python/env/bin/pip install cython
	@./.python/env/bin/pip install hivtrace==0.3.2

npm:
	echo "running npm"
	@npm install

directories:
	mkdir -p app/absrel/output
	mkdir -p app/bgm/output
	mkdir -p app/busted/output
	mkdir -p app/fade/output
	mkdir -p app/fel/output
	mkdir -p app/flea/output
	mkdir -p app/fubar/output
	mkdir -p app/fade/output
	mkdir -p app/gard/output
	mkdir -p app/meme/output
	mkdir -p app/multihit/output
	mkdir -p app/nrm/output
	mkdir -p app/prime/output
	mkdir -p app/relax/output
	mkdir -p app/slac/output
	mkdir -p app/hivtrace/output

install: hyphy hyphy-analyses hivtrace npm directories