# Top level Makefile for HMMER3 # # On most systems, to build H3 you should only need: # % ./configure; make # # Optionally, you can run a test suite: # % make check # # And optionally, you can install everything more permanently: # % make install # # For more information, see the Installation chapter of the HMMER # User's Guide. # # VPATH and shell configuration # top_srcdir = . srcdir = . SHELL = /bin/sh # location of easel ESLDIR = easel # location of libdivsufsort for suffix array creation SADIR = libdivsufsort # Package information # PACKAGE = HMMER PACKAGE_VERSION = 3.1b2 PACKAGE_TARNAME = hmmer # Installation targets # prefix = /usr/local exec_prefix = ${prefix} datarootdir = ${prefix}/share bindir = ${exec_prefix}/bin libdir = ${exec_prefix}/lib includedir = ${prefix}/include mandir = ${datarootdir}/man docdir = ${datarootdir}/doc/${PACKAGE_TARNAME} pdfdir = ${docdir} mandir = ${datarootdir}/man man1dir = ${mandir}/man1 man1ext = .1 # Compiler configuration # CC = gcc -std=gnu99 CFLAGS = -O3 -fomit-frame-pointer -fstrict-aliasing -march=core2 -pthread -fPIC LDFLAGS = -static SIMDFLAGS = -msse2 CPPFLAGS = # Other tools # AR = /usr/bin/ar RANLIB = ranlib INSTALL = /usr/bin/install -c # beautification magic stolen from git # QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c QUIET_SUBDIR1 = ifndef V QUIET_CC = @echo ' ' CC $@; QUIET_GEN = @echo ' ' GEN $@; QUIET_AR = @echo ' ' AR $@; QUIET_SUBDIR0 = +@subdir= QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \ ${MAKE} -C $$subdir endif # Programs installed by HMMER (stable, documented) # PROGS = alimask\ hmmalign\ hmmbuild\ hmmconvert\ hmmemit\ hmmfetch\ hmmpress\ hmmscan\ hmmsearch\ hmmsim\ hmmstat\ jackhmmer\ phmmer\ nhmmer\ nhmmscan\ hmmpgmd .PHONY: all dev check pdf install uninstall clean distclean TAGS # all: Compile all documented executables. # (Excludes test programs.) # all: ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} all ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} all # dev: compile all executables, including drivers. # dev: ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} dev # tests: compile all test drivers for 'make check' # tests: ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests # check: Run test suites. # check: ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check # pdf: compile the User Guides. # pdf: ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf # install: installs the binaries in ${bindir}/ # When man pages are done, will install man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1) # Creates these directories if they don't exist. # Prefix those paths with ${DESTDIR} (rarely used, usually null; # may be set on a make command line when building contrib RPMs). install: ${INSTALL} -d ${DESTDIR}${bindir} ${INSTALL} -d ${DESTDIR}${libdir} ${INSTALL} -d ${DESTDIR}${includedir} ${INSTALL} -d ${DESTDIR}${man1dir} ${INSTALL} -d ${DESTDIR}${pdfdir} ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} install # uninstall: Reverses the steps of "make install". # uninstall: ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} uninstall ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} uninstall # "make clean" removes almost everything except configuration files. # clean: ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} clean -rm -f *.o *~ Makefile.bak core TAGS gmon.out # "make distclean" leaves a pristine source distribution. # distclean: ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}profmark ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} distclean ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} distclean -rm config.log config.status -rm -rf autom4te.cache -rm -f *.o *~ Makefile.bak core TAGS gmon.out -rm -f cscope.po.out cscope.out cscope.in.out cscope.files -rm -f src/impl -rm Makefile #Use 'ifneq' instead of 'test -e' because the '+@' in QUIET_SUBDIR0 can't #be passed to the shell. Note that ifneq breaks if indented. ifneq (,$(wildcard ./release-notes/LICENSE.sh)) -rm -f release-notes/LICENSE.sh endif TAGS: -rm -f ${top_srcdir}/TAGS make tags-append tags-append: etags -o ${top_srcdir}/TAGS -a ${srcdir}/Makefile.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/COPYRIGHT etags -o ${top_srcdir}/TAGS -a ${srcdir}/INSTALL etags -o ${top_srcdir}/TAGS -a ${srcdir}/LICENSE etags -o ${top_srcdir}/TAGS -a ${srcdir}/README etags -o ${top_srcdir}/TAGS -a ${srcdir}/configure.ac etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.h etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.pl etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.h etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.h etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.h etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.man etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/boilerplate-tail etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.tex etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/README etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/00README etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.c etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/x-* etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/pmark-* etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.in etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pl etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sh etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pm etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sqc ${QUIET_SUBDIR0}easel ${QUIET_SUBDIR1} tags-append ################################################################ # HMMER - Biological sequence analysis with profile HMMs # Version 3.1b2; February 2015 # Copyright (C) 2015 Howard Hughes Medical Institute. # Other copyrights also apply. See the COPYRIGHT file for a full list. # # HMMER is distributed under the terms of the GNU General Public License # (GPLv3). See the LICENSE file for details. # # SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/Makefile.in $ # SVN $Id: Makefile.in 4489 2013-06-19 02:46:43Z wheelert $ ################################################################