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| # Top level Makefile for Infernal | |
| # | |
| # On most systems, to build Infernal 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 Infernal | |
| # User's Guide. | |
| # | |
| # VPATH and shell configuration | |
| # | |
| top_srcdir = @top_srcdir@ | |
| srcdir = @srcdir@ | |
| VPATH = @srcdir@ | |
| SHELL = /bin/sh | |
| # location of easel | |
| ESLDIR = @INFERNAL_ESLDIR@ | |
| # location of hmmer | |
| HMMERDIR = @INFERNAL_HMMERDIR@ | |
| # location of suffix array library | |
| SADIR = @INFERNAL_SADIR@ | |
| # impl directory (currently only either 'impl_sse' or '') | |
| IMPLDIR = @INFERNAL_IMPLDIR@ | |
| # Package information | |
| # | |
| PACKAGE = @PACKAGE_NAME@ | |
| PACKAGE_VERSION = @PACKAGE_VERSION@ | |
| PACKAGE_TARNAME = @PACKAGE_TARNAME@ | |
| # Installation targets | |
| # | |
| prefix = @prefix@ | |
| exec_prefix = @exec_prefix@ | |
| datarootdir = @datarootdir@ | |
| bindir = @bindir@ | |
| libdir = @libdir@ | |
| includedir = @includedir@ | |
| docdir = @docdir@ | |
| pdfdir = @pdfdir@ | |
| mandir = @mandir@ | |
| man1dir = ${mandir}/man1 | |
| man1ext = .1 | |
| # Compiler configuration | |
| # | |
| CC = @CC@ | |
| CFLAGS = @CFLAGS@ | |
| LDFLAGS = -static @LDFLAGS@ | |
| SIMDFLAGS = @SIMD_CFLAGS@ | |
| CPPFLAGS = @CPPFLAGS@ | |
| # Other tools | |
| # | |
| AR = @AR@ | |
| RANLIB = @RANLIB@ | |
| INSTALL = @INSTALL@ | |
| # beautification magic stolen from git | |
| # | |
| QUIET_SUBDIR0 = +${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 Infernal | |
| # | |
| PROGS = cmalign\ | |
| cmbuild\ | |
| cmcalibrate\ | |
| cmemit\ | |
| cmfetch\ | |
| cmscan\ | |
| cmsearch\ | |
| cmstat | |
| SSEPROGS = sse_cmsearch\ | |
| cmsearch_dual | |
| .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 | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} all | |
| ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} all | |
| ${QUIET_SUBDIR0}rmark ${QUIET_SUBDIR1} all | |
| ifdef IMPLDIR | |
| ${QUIET_SUBDIR0}src/impl_sse ${QUIET_SUBDIR1} all | |
| endif | |
| # dev: compile all executables, including drivers. | |
| # | |
| dev: | |
| ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} dev | |
| ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} dev | |
| ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} dev | |
| ${QUIET_SUBDIR0}rmark ${QUIET_SUBDIR1} all | |
| # tests: compile all test drivers for 'make check' | |
| # | |
| tests: | |
| ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests | |
| ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} tests | |
| ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests | |
| # check: Run test suites. | |
| # | |
| # We do a 'check' in HMMERDIR/testsuite, not HMMERDIR/ because we | |
| # don't need to run the Easel testsuite twice. | |
| # | |
| # Also, HMMER's 'make check' requires its own easel subdir complete | |
| # with compiled miniapps. This may or may not exist. In working copies | |
| # of the trunk it will exist but won't be compiled (infernal/hmmer/ | |
| # will use infernal/easel, not infernal/hmmer/easel). In a released | |
| # version infernal/hmmer/easel won't even exist since we delete it | |
| # prior to creating a release. So, we take care to have the calling | |
| # of hmmer's testsuite work in either case. If hmmer/easel/ exists we | |
| # copy the required miniapps into it and run 'make check' from | |
| # hmmer/testsuite then delete them. If it doesn't, we create a symlink | |
| # to infernal/easel as infernal/hmmer/easel then we run the testsuite | |
| # and then we delete the symlink. Also, if srcdir/hmmer/easel doesn't | |
| # exist, we symlink it to srcdir/easel because the hmmer testsuite | |
| # needs easel/formats/BLOSUM62 which will only be in srcdir/easel | |
| # (yuck!). | |
| check: | |
| ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} tests | |
| ${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} all | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} tests | |
| ${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} tests | |
| ${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} check | |
| if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-afetch; then cp ${ESLDIR}/miniapps/esl-afetch ${HMMERDIR}/easel/miniapps; fi | |
| if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-reformat; then cp ${ESLDIR}/miniapps/esl-reformat ${HMMERDIR}/easel/miniapps; fi | |
| if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-sfetch; then cp ${ESLDIR}/miniapps/esl-sfetch ${HMMERDIR}/easel/miniapps; fi | |
| if test -d ${HMMERDIR}/easel && ! test -e ${HMMERDIR}/easel/miniapps/esl-sfetch; then cp ${ESLDIR}/miniapps/esl-shuffle ${HMMERDIR}/easel/miniapps; fi | |
| if ! test -d ${HMMERDIR}/easel; then cd ${HMMERDIR}; @LN_S@ ../${ESLDIR} .; cd ..; fi | |
| if ! test -d ${srcdir}/${HMMERDIR}/easel; then @LN_S@ ${srcdir}/${ESLDIR} ${srcdir}/${HMMERDIR}/easel; fi | |
| ${QUIET_SUBDIR0}${HMMERDIR}/testsuite ${QUIET_SUBDIR1} check | |
| if test -L ${HMMERDIR}/easel; then rm ${HMMERDIR}/easel; fi | |
| if test -L ${srcdir}/${HMMERDIR}/easel; then rm ${srcdir}/${HMMERDIR}/easel; fi | |
| if test -e ${HMMERDIR}/easel/miniapps/esl-afetch; then rm ${HMMERDIR}/easel/miniapps/esl-afetch; fi | |
| if test -e ${HMMERDIR}/easel/miniapps/esl-reformat; then rm ${HMMERDIR}/easel/miniapps/esl-reformat; fi | |
| if test -e ${HMMERDIR}/easel/miniapps/esl-sfetch; then rm ${HMMERDIR}/easel/miniapps/esl-sfetch; fi | |
| if test -e ${HMMERDIR}/easel/miniapps/esl-shuffle; then rm ${HMMERDIR}/easel/miniapps/esl-shuffle; fi | |
| ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check | |
| # devcheck: Run Infernal developer test suite (slower, but more comprehensive than 'check'). | |
| # | |
| devcheck: | |
| ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} devcheck | |
| # 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 ${DESTDIR}${man1dir} | |
| ${INSTALL} -d ${DESTDIR}${pdfdir} | |
| # src 'install' moves into impl_sse and does 'install' (if IMPLDIR is defined (system has SSE)) | |
| ${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}rmark ${QUIET_SUBDIR1} clean | |
| ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean | |
| ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} clean | |
| ${QUIET_SUBDIR0}${ESLDIR} ${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}rmark ${QUIET_SUBDIR1} distclean | |
| ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean | |
| ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean | |
| ${QUIET_SUBDIR0}${HMMERDIR} ${QUIET_SUBDIR1} distclean | |
| # no need to distclean in easel/ because distclean in hmmer/ already did that (and easel/Makefile has been deleted) | |
| -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 release-notes/LICENSE.sh | |
| -rm -f src/impl | |
| -rm Makefile | |
| # "make TAGS": emacs etags database, for searching the whole source tree. | |
| TAGS: | |
| ./makeTAGS.sh | |