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Makefile
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############################################################################################################
# AnnotSV 3.4.4 #
# #
# AnnotSV: An integrated tool for Structural Variations annotation and ranking #
# #
# Copyright (C) 2017-2024 Veronique Geoffroy (veronique.geoffroy@inserm.fr) #
# #
# This is part of AnnotSV source code. #
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License #
# as published by the Free Software Foundation; either version 3 #
# of the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; If not, see <http://www.gnu.org/licenses/>. #
############################################################################################################
SHELL = /bin/bash
DESTDIR ?=
PREFIX ?= /usr/local
INSTALLDIR1 := $(shell readlink -f "$(DESTDIR)$(PREFIX)")
INSTALLDIR2 := $(shell readlink -f "$(DESTDIR).")
BINDIR := $(PREFIX)/bin
ETCDIR := $(PREFIX)/etc
SHAREDIR := $(PREFIX)/share
DOCDIR := $(SHAREDIR)/doc
BASHDIR := $(SHAREDIR)/bash
TESTSDIR := $(PREFIX)/tests
TCLVERSION := tcl$(shell echo 'puts $${tcl_version};exit 0' | tclsh)
TCLDIRDISTRIBUTED := share/tcl
TCLDIR := $(SHAREDIR)/$(TCLVERSION)
PYTHONDIR := $(SHAREDIR)/python3
ANNOTSV := AnnotSV
VERSION := 3.4.4
RM := /bin/rm
RMDIR := /bin/rmdir
MKDIR := install -d
MV := /bin/mv
CP := install -p -m 0644
CPDIR := /bin/cp -r
CHMOD := /bin/chmod -R 777
CONFIGFILE := etc/$(ANNOTSV)/configfile
MAKEFILE := Makefile
PROPERTIES := etc/$(ANNOTSV)/application.properties
BASH_SCRIPTS := $(shell find share/bash/$(ANNOTSV)/ -name '*.bash' 2> /dev/null)
DOCUMENTATIONS := $(shell find License.txt changeLog.txt commandLineOptions.txt README.AnnotSV_*.pdf 2> /dev/null)
# make install
.PHONY: install
ifeq ('$(INSTALLDIR1)' , '$(INSTALLDIR2)')
all: install-display install-documentationlight install-variantconvert install-done
install: install-display install-documentationlight install-variantconvert install-done
install-exomiser: install-exomiser-1 install-exomiser-3
else
all: install-display install-configfile install-makefile install-executable install-tcl-toolbox install-python-toolbox install-bash-toolbox install-doc install-others-doc install-variantconvert install-done
install: install-display install-configfile install-makefile install-executable install-tcl-toolbox install-python-toolbox install-bash-toolbox install-doc install-others-doc install-variantconvert install-done
install-exomiser: install-exomiser-1 install-exomiser-2 install-exomiser-3
endif
install-display:
@echo ""
@echo "Installation of $(ANNOTSV)-$(VERSION):"
@echo "----------------------------"
@echo DESTDIR=$(DESTDIR)
@echo PREFIX=$(PREFIX)
@echo TCLVERSION=$(TCLVERSION)
install-documentationlight: $(DOCUMENTATIONS)
@echo ""
$(MV) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
$(MV) $(TCLDIRDISTRIBUTED) $(TCLDIR)
install-configfile: $(CONFIGFILE)
@echo ""
@echo "Configfile configuration"
@echo "------------------------"
$(MKDIR) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
install -p -m 0755 $(CONFIGFILE) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
install-makefile: $(MAKEFILE)
@echo ""
@echo "Makefile installation"
@echo "---------------------"
install -p -m 0755 $(MAKEFILE) $(DESTDIR)$(PREFIX)
install-executable:
@echo ""
@echo "Executable installation"
@echo "-----------------------"
$(MKDIR) $(DESTDIR)$(BINDIR)
install -p -m 0755 bin/AnnotSV $(DESTDIR)$(BINDIR)
install-tcl-toolbox:
@echo ""
@echo "Tcl scripts installation"
@echo "------------------------"
$(MKDIR) $(DESTDIR)$(TCLDIR)/$(ANNOTSV)
cd share/tcl ; tar cf - $(ANNOTSV) | tar xf - -C $(DESTDIR)$(TCLDIR)/
install-python-toolbox:
@echo ""
@echo "Python scripts installation"
@echo "---------------------------"
$(MKDIR) $(DESTDIR)$(PYTHONDIR)/variantconvert
cd share/python3 ; tar cf - variantconvert | tar xf - -C $(DESTDIR)$(PYTHONDIR)/
install-variantconvert:
@echo ""
@echo "variantconvert installation"
@echo "---------------------------"
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/pipinstall.flag
chmod 777 $(DESTDIR)$(PYTHONDIR)/variantconvert/pipinstall.flag
pip3 install -e $(DESTDIR)$(PYTHONDIR)/variantconvert/. &> ./tmp.variantconvert.txt || pip install -e $(DESTDIR)$(PYTHONDIR)/variantconvert/. &> ./tmp.variantconvert.txt || rm -f $(DESTDIR)$(PYTHONDIR)/variantconvert/pipinstall.flag
rm -f ./tmp.variantconvert.txt
ls -l $(DESTDIR)$(PYTHONDIR)/variantconvert/pipinstall.flag || echo "variantconvert not installed"
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.combined.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.full.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.fullsplit.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.combined.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.full.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.fullsplit.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.combined.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.full.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.fullsplit.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.combined.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.full.local.json
touch $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.fullsplit.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.combined.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.full.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_bed.fullsplit.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.combined.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.full.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh37/annotsv3_from_vcf.fullsplit.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.combined.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.full.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_bed.fullsplit.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.combined.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.full.local.json
$(CHMOD) $(DESTDIR)$(PYTHONDIR)/variantconvert/src/variantconvert/configs/GRCh38/annotsv3_from_vcf.fullsplit.local.json
install-bash-toolbox: $(BASH_SCRIPTS)
@echo ""
@echo "Bash scripts installation"
@echo "-------------------------"
$(MKDIR) $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
$(CP) $^ $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
install-doc: $(DOCUMENTATIONS)
@echo ""
@echo "Documentations installation"
@echo "---------------------------"
$(MKDIR) $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
$(CP) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
install-others-doc: share/doc/$(ANNOTSV)/Example
$(CPDIR) $^ $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
install-done:
@echo ""
@echo "Done"
@echo ""
@echo "WARNING: Annotations need to be installed:"
@echo "make DESTDIR=$(DESTDIR) PREFIX=$(PREFIX) install-human-annotation"
@echo "make DESTDIR=$(DESTDIR) PREFIX=$(PREFIX) install-mouse-annotation"
# make install_organism_annotations
install-all-annotations: install-human-annotation install-mouse-annotation
install-human-annotation: Annotations_Human_$(VERSION).tar.gz install-exomiser
@echo ""
@echo "Installation of human annotation:"
@echo ""
tar -xf Annotations_Human_$(VERSION).tar.gz -C $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
$(RM) -rf Annotations_Human_$(VERSION).tar.gz
$(CHMOD) $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_*
@echo ""
@echo "--> Human annotation installed"
install-exomiser-1: 2309_phenotype.zip
@echo ""
@echo "Installation of Exomiser data:"
@echo ""
$(MKDIR) -p $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2309
tar -xf 2309_hg19.tar.gz -C $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2309/
unzip 2309_phenotype.zip -d $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/Annotations_Exomiser/2309/
$(RM) -rf 2309_phenotype.zip
$(RM) -rf 2309_hg19.tar.gz
install-exomiser-2:
install -p -m 0755 $(PROPERTIES) $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
$(CPDIR) share/AnnotSV/jar/ $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
install-exomiser-3:
@echo ""
@echo "--> Exomiser data installed"
install-mouse-annotation: Annotations_Mouse_$(VERSION).tar.gz
@echo ""
@echo "Installation of mouse annotation:"
@echo ""
$(MKDIR) $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
tar -xf Annotations_Mouse_$(VERSION).tar.gz -C $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)/
$(RM) -rf Annotations_Mouse_$(VERSION).tar.gz
@echo ""
@echo "--> Mouse annotation installed"
Annotations_%.tar.gz:
@echo ""
@echo "Download AnnotSV supporting data files:"
@echo ""
curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/$@
%_phenotype.zip:
@echo ""
@echo "Download Exomiser supporting data files:"
@echo ""
curl -C - -LO https://www.lbgi.fr/~geoffroy/Annotations/2309_hg19.tar.gz
curl -C - -LO https://data.monarchinitiative.org/exomiser/data/$@
# make uninstall
.PHONY: uninstall
ifeq ('$(PREFIX)' , '/usr/local')
uninstall: uninstall1 uninstall4
else ifeq ('$(INSTALLDIR1)' , '$(INSTALLDIR2)')
uninstall: uninstall1 uninstall2 uninstall4
else
uninstall: uninstall1 uninstall2 uninstall3 uninstall4
endif
uninstall1:
@echo ""
@echo "Uninstalling of $(ANNOTSV)"
@echo "------------------------"
$(RM) -f $(DESTDIR)$(BINDIR)/$(ANNOTSV)
$(RM) -f $(DESTDIR)$(BINDIR)/INSTALL_annotations.sh
$(RM) -f $(DESTDIR)$(BINDIR)/INSTALL_code.sh
$(RM) -rf $(DESTDIR)$(TCLDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PYTHONDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PYTHONDIR)/variantconvert
$(RM) -rf $(DESTDIR)$(DOCDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(SHAREDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(BASHDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(ETCDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(TESTSDIR)/$(ANNOTSV)
$(RM) -rf $(DESTDIR)$(PREFIX)/Makefile
$(RM) -rf $(DESTDIR)$(PREFIX)/README.md
$(RM) -rf $(DESTDIR)$(PREFIX)/Scoring_Criteria_AnnotSV_*.xlsx
$(RM) -rf $(DESTDIR)$(PREFIX)/.git
$(RM) -rf $(DESTDIR)$(PREFIX)/.gitignore
uninstall2:
$(RMDIR) --ignore-fail-on-non-empty $(DESTDIR)$(BINDIR) $(DESTDIR)$(BASHDIR) $(DESTDIR)$(TCLDIR) $(DESTDIR)$(PYTHONDIR) $(DESTDIR)$(DOCDIR) $(DESTDIR)$(SHAREDIR) $(DESTDIR)$(ETCDIR) $(DESTDIR)$(TESTSDIR)
uninstall3:
$(RMDIR) --ignore-fail-on-non-empty $(DESTDIR)$(PREFIX)
uninstall4:
@echo ""
@echo "Done"