diff --git a/Makefile b/Makefile index f803ee0..e1b57ef 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ PREFIX := $(PWD) PROFILE := $(HOME)/.bashrc -VERSION := 1.0.3 +VERSION := 1.0.4 PROJECT := "setTestProject" NUMCPUS := 1 SHELL := /bin/bash @@ -48,10 +48,10 @@ install: install-prerequisites @echo "'make env' performs this step for you" @echo "DONE: installation of Lyve-SET v$(VERSION) complete." -install-prerequisites: install-mkdir install-vcftools install-CGP install-SGELK install-varscan install-phast install-phispy install-samtools install-bcftools install-smalt install-snap install-raxml install-quake +install-prerequisites: install-mkdir install-vcftools install-CGP install-SGELK install-varscan install-phast install-phispy install-samtools install-bcftools install-smalt install-snap install-raxml @echo DONE installing prerequisites -clean: clean-tmp clean-symlinks clean-vcftools clean-CGP clean-SGELK clean-varscan clean-phast clean-phispy clean-samtools clean-bcftools clean-smalt clean-snap clean-raxml clean-quake +clean: clean-tmp clean-symlinks clean-vcftools clean-CGP clean-SGELK clean-varscan clean-phast clean-phispy clean-samtools clean-bcftools clean-smalt clean-snap clean-raxml @echo "Remember to remove the line with PATH and Lyve-SET from $(PROFILE)" install-mkdir: @@ -188,6 +188,14 @@ install-quake: clean-quake: cd $(PREFIX)/scripts && rm -vf build_bithash count-kmers cov_model.py cov_model.r quake.py correct count-qmers cov_model_qmer.r kmer_hist.r +install-edirect: + cd $(PREFIX)/build && perl -MNet::FTP -e '$$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $$ftp->login; $$ftp->binary; $$ftp->get("/entrez/entrezdirect/edirect.zip");' && unzip -u -q edirect.zip && rm edirect.zip + cd $(PREFIX)/build/edirect && sh setup.sh + mv -v $(PREFIX)/build/edirect $(PREFIX)/lib + +clean-edirect: + rm -rvf $(PREFIX)/lib/edirect + cuttingedge: install-mkdir cuttingedge-gitclone install-prerequisites @echo "DONE installing the cutting edge version"