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DEFAULT_G=homo-sapiens.g

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DIRS=homo-sapiens/ mus-musculus/ rattus-norvegicus/
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GERMLINE_JS=../browser/js/germline.js
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all: get-saved-data
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germline: get-saved-data $(GERMLINE_JS)
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js: $(GERMLINE_JS)
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$(GERMLINE_JS): $(DEFAULT_G)
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	python buildBrowserGermline.py $(DEFAULT_G) $@
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get-all-data: clean
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	sh get-germline
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	python get-CD.py
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get-saved-data: germline_id
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	sh get-saved-germline
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clean:
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	rm -rf $(DIRS) $(GERMLINE_JS) 
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diff-from-saved:
	rm -rf saved-germline
	mkdir saved-germline
	cd saved-germline ; sh ../get-saved-germline
	echo
	diff -r -u -x "*[.][^f][^a]" -x "germline*" -x "get*" -x "Makefile" -x "saved-*" saved-germline/ .
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tests:
	python split-from-imgt.py --test
	make -C tests


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distrib: get-all-data js
	cd .. ; tar cvzf germline-`cat germline/germline_id`.tar.gz germline/germline_id germline/*/*.fa germline/IMGT_RELEASE browser/js/germline.js

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.PHONY: all germline js get-all-data clean diff-from-saved tests