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| all: PhyloCSF | |
| .PHONY: PhyloCSF CamlPaml twt cde-package clean | |
| ARCH := $(shell uname).$(shell uname -m) | |
| PHYLOCSF_BASE := $(shell pwd) | |
| export PHYLOCSF_BASE | |
| PhyloCSF: CamlPaml | |
| cd src; $(MAKE) clean; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS) | |
| cp src/_build/PhyloCSF.native PhyloCSF.$(ARCH) | |
| CamlPaml: twt/ocaml+twt | |
| cd lib/CamlPaml; PATH=$(PATH):$(CURDIR)/twt $(MAKE) $(MFLAGS) reinstall | |
| twt/ocaml+twt: twt/ocaml+twt.ml | |
| cd twt && $(MAKE) | |
| twt/ocaml+twt.ml: | |
| git submodule update --init twt | |
| cde-package: PhyloCSF CDE/cde | |
| rm -rf cde-package cde-package.$(ARCH) | |
| CDE/cde ./PhyloCSF.$(ARCH) 12flies PhyloCSF_Examples/tal-AA.fa | |
| CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/ALDH2.exon5.fa --frames=3 --allScores | |
| CDE/cde ./PhyloCSF.$(ARCH) 29mammals PhyloCSF_Examples/Aldh2.mRNA.fa --strategy=fixed --frames=3 --orf=ATGStop --minCodons=400 --allScores --removeRefGaps --aa | |
| mv cde-package cde-package.$(ARCH) | |
| tar -cf cde-package.$(ARCH).tar cde-package.$(ARCH) | |
| CDE/cde: | |
| git submodule update --init CDE | |
| cd CDE && $(MAKE) | |
| clean: | |
| (cd CDE; $(MAKE) clean) || true | |
| cd lib/CamlPaml; $(MAKE) clean | |
| cd src; $(MAKE) clean | |
| rm -f PhyloCSF.* | |
| rm -rf cde-package* | |
| cleaner: clean | |
| rm -rf twt CDE || true |