Index: head/biology/mafft/Makefile =================================================================== --- head/biology/mafft/Makefile (revision 404404) +++ head/biology/mafft/Makefile (revision 404405) @@ -1,70 +1,47 @@ # Created by: Fernan Aguero # $FreeBSD$ PORTNAME= mafft -PORTVERSION= 7.221 +PORTVERSION= 7.266 CATEGORIES= biology MASTER_SITES= http://mafft.cbrc.jp/alignment/software/ DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src MAINTAINER= cartwright@asu.edu COMMENT= Multiple alignment program for amino acid or nucleotide sequences LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/license OPTIONS_DEFINE= DOCS EXAMPLES WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-without-extensions BUILD_WRKSRC= ${WRKSRC}/core +INSTALL_WRKSRC= ${WRKSRC}/core USES= gmake shebangfix tar:tgz -SHEBANG_FILES= core/mafftash_premafft.tmpl core/seekquencer_premafft.tmpl +SHEBANG_FILES= core/*.tmpl -LIBEXEC_FILES= dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ - pair2hat3s multi2hat3s pairash addsingle splittbfast \ - disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap \ - countlen seq2regtable regtable2seq score getlag dndpre \ - setcore replaceu restoreu setdirection makedirectionlist version -PERL_LIBEXEC_FILES= mafftash_premafft.pl seekquencer_premafft.pl -SCRIPT_FILES= mafft mafft-homologs.rb -LN_FILES= einsi fftns fftnsi ginsi linsi mafft-einsi mafft-fftns \ - mafft-fftnsi mafft-ginsi mafft-linsi mafft-nwns mafft-nwnsi \ - mafft-qinsi mafft-xinsi nwns nwnsi -MAN1_FILES= mafft.1 mafft-homologs.1 +MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ + INSTALL_DATA="${INSTALL_DATA}" \ + INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ + INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ + MKDIR="${MKDIR}" \ + LN="${LN}" -BROKEN_sparc64= Does not install on sparc64: depends on thread-local storage +.include post-patch: - @${REINPLACE_CMD} -e 's|^PREFIX = .*$$||' \ - -e 's|^MANDIR = .*$$|MANDIR = $$(MANPREFIX)/man/man1|' \ - -e 's|^CC = .*$$||' \ - -e 's|^CFLAGS = .*$$||' \ +.if ${ARCH} == sparc64 + @${REINPLACE_CMD} -e 's|ENABLE_MULTITHREAD = -Denablemultithread||' \ ${BUILD_WRKSRC}/Makefile +.endif -do-install: - @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} -.for exec in ${LIBEXEC_FILES} - ${INSTALL_PROGRAM} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} -.endfor -.for exec in ${PERL_LIBEXEC_FILES} - ${INSTALL_SCRIPT} ${WRKSRC}/binaries/${exec} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} -.endfor -.for exec in ${SCRIPT_FILES} - ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${exec} ${STAGEDIR}${PREFIX}/bin -.endfor -.for exec in ${LN_FILES} - ${LN} -sf mafft ${STAGEDIR}${PREFIX}/bin/${exec} -.endfor - ${LN} -sf ../libexec/${PORTNAME}/mafft-distance ${STAGEDIR}${PREFIX}/bin/mafft-distance - ${LN} -sf ../libexec/${PORTNAME}/mafft-profile ${STAGEDIR}${PREFIX}/bin/mafft-profile -.for man in ${MAN1_FILES} - ${INSTALL_MAN} ${WRKSRC}/binaries/${man} ${STAGEDIR}${MAN1PREFIX}/man/man1 -.endfor +post-install: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - ${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR} @${MKDIR} ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/test/* ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/readme ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/license ${STAGEDIR}${DOCSDIR} .include Index: head/biology/mafft/distinfo =================================================================== --- head/biology/mafft/distinfo (revision 404404) +++ head/biology/mafft/distinfo (revision 404405) @@ -1,2 +1,2 @@ -SHA256 (mafft-7.221-without-extensions-src.tgz) = 6d9cdcc04684c8c8ff61888dffc0396b48c713e4519a99f54e04c4a7179d2776 -SIZE (mafft-7.221-without-extensions-src.tgz) = 376075 +SHA256 (mafft-7.266-without-extensions-src.tgz) = 59d4921e13377bb2c8e1f0a007e94b3e698e2c546ce8facc9daa530bc673e707 +SIZE (mafft-7.266-without-extensions-src.tgz) = 440576 Index: head/biology/mafft/files/patch-core_Makefile =================================================================== --- head/biology/mafft/files/patch-core_Makefile (nonexistent) +++ head/biology/mafft/files/patch-core_Makefile (revision 404405) @@ -0,0 +1,103 @@ +--- core/Makefile.orig 2015-11-26 01:42:39 UTC ++++ core/Makefile +@@ -1,8 +1,7 @@ +-PREFIX = /usr/local +-LIBDIR = $(PREFIX)/libexec/mafft +-BINDIR = $(PREFIX)/bin +-MANDIR = $(PREFIX)/share/man/man1 +-DESTDIR = ++prefix = ${STAGEDIR}${PREFIX} ++LIBDIR = $(prefix)/libexec/mafft ++BINDIR = $(prefix)/bin ++MANDIR = $(prefix)/man/man1 + + #MNO_CYGWIN = -mno-cygwin + +@@ -10,29 +9,17 @@ ENABLE_MULTITHREAD = -Denablemultithread + # Comment out the above line if your compiler + # does not support TLS (thread-local strage). + +-CC = gcc +-CFLAGS = -O3 +-#CFLAGS = -O3 -fPIC +-# add -fPIC when building .so files +- +-#CC = icc +-#CFLAGS = -fast +-# if you have icc, use this. +- +-#CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 +-#CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 -fprofile-arcs -ftest-coverage +-#CFLAGS = -O0 -fPIC -pedantic -Wall -std=c99 -g -DMALLOC_CHECK_=3 # for shark, valgrind +- +- +-MYCFLAGS = $(MNO_CYGWIN) $(ENABLE_MULTITHREAD) $(CFLAGS) ++MYCFLAGS = $(ENABLE_MULTITHREAD) $(CFLAGS) + + ifdef ENABLE_MULTITHREAD +-LIBS = -lm -lpthread ++LIBS = -lm -pthread + else + LIBS = -lm + endif + +-INSTALL = install ++LNFILES = linsi ginsi fftns fftnsi nwns nwnsi einsi \ ++ mafft-linsi mafft-ginsi mafft-fftns mafft-fftnsi mafft-nwns \ ++ mafft-nwnsi mafft-einsi mafft-xinsi mafft-qinsi + + PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign \ + pair2hat3s multi2hat3s pairash addsingle \ +@@ -131,12 +118,6 @@ MANPAGES = mafft.1 mafft-homologs.1 + + + all : $(PERLPROGS) $(PROGS) $(SCRIPTS) +- cp $(SCRIPTS) ../scripts +- chmod 755 ../scripts/* +- cp $(PERLPROGS) $(PROGS) ../binaries +- chmod 755 ../binaries/* +- cp $(MANPAGES) ../binaries +- @echo done. + + sos : $(SOS) + dylibs : $(DYLIBS) +@@ -524,31 +505,13 @@ clean : + # rm -f ../binaries/* ../scripts/* + + install : all +- mkdir -p $(DESTDIR)$(LIBDIR) +- chmod 755 $(DESTDIR)$(LIBDIR) +- mkdir -p $(DESTDIR)$(BINDIR) +- chmod 755 $(DESTDIR)$(BINDIR) +- chmod 755 $(SCRIPTS) +- $(INSTALL) $(SCRIPTS) $(DESTDIR)$(BINDIR) +- chmod 755 $(PROGS) ||: # in MinGW, it's ok if this fails +- $(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR) +- $(INSTALL) $(PERLPROGS) $(DESTDIR)$(LIBDIR) +- $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(LIBDIR) ++ $(MKDIR) $(DESTDIR)$(LIBDIR) $(DESTDIR)$(BINDIR) $(DESTDIR)$(MANDIR) ++ $(INSTALL_SCRIPT) $(SCRIPTS) $(DESTDIR)$(BINDIR) ++ $(INSTALL_PROGRAM) $(PROGS) $(DESTDIR)$(LIBDIR) ++ $(INSTALL_SCRIPT) $(PERLPROGS) $(DESTDIR)$(LIBDIR) ++ $(INSTALL_DATA) $(MANPAGES) $(DESTDIR)$(MANDIR) + +- ( cd $(DESTDIR)$(BINDIR); \ +-rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ +-rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ +-ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ +-ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ +-ln -s mafft einsi; \ +-ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ +-ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ +-ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ +-rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \ +-rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . ) ++ $(foreach f,$(LNFILES),$(LN) -s mafft $(DESTDIR)$(BINDIR)/$(f);) + +- mkdir -p $(DESTDIR)$(MANDIR) +- chmod 755 $(DESTDIR)$(MANDIR) +- $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(MANDIR) +-# remove incorrectly installed manpages by previous versions +-# rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1 ++ $(LN) -s ../libexec/mafft/mafft-profile $(DESTDIR)$(BINDIR)/mafft-profile ++ $(LN) -s ../libexec/mafft/mafft-distance $(DESTDIR)$(BINDIR)/mafft-distance Property changes on: head/biology/mafft/files/patch-core_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/mafft/files/patch-core_mltaln.h =================================================================== --- head/biology/mafft/files/patch-core_mltaln.h (nonexistent) +++ head/biology/mafft/files/patch-core_mltaln.h (revision 404405) @@ -0,0 +1,11 @@ +--- core/mltaln.h.orig 2015-11-26 01:42:39 UTC ++++ core/mltaln.h +@@ -182,6 +182,8 @@ extern int conjuctionfortbfast(); + extern int fastconjuction(); + extern char seqcheck( char ** ); + ++extern int deletenewinsertions_whole_eq( int on, int an, char **oseq, char **aseq, int **deletelist ); ++ + typedef struct _LocalHom + { + int nokori; Property changes on: head/biology/mafft/files/patch-core_mltaln.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/mafft/pkg-plist =================================================================== --- head/biology/mafft/pkg-plist (revision 404404) +++ head/biology/mafft/pkg-plist (revision 404405) @@ -1,67 +1,67 @@ bin/einsi bin/fftns bin/fftnsi bin/ginsi bin/linsi bin/mafft bin/mafft-distance bin/mafft-einsi bin/mafft-fftns bin/mafft-fftnsi bin/mafft-ginsi bin/mafft-homologs.rb bin/mafft-linsi bin/mafft-nwns bin/mafft-nwnsi bin/mafft-profile bin/mafft-qinsi bin/mafft-xinsi bin/nwns bin/nwnsi libexec/mafft/addsingle libexec/mafft/contrafoldwrap libexec/mafft/countlen libexec/mafft/disttbfast libexec/mafft/dndblast libexec/mafft/dndfast7 libexec/mafft/dndpre libexec/mafft/dvtditr libexec/mafft/f2cl libexec/mafft/getlag libexec/mafft/mafft-distance libexec/mafft/mafft-profile libexec/mafft/mafftash_premafft.pl libexec/mafft/makedirectionlist libexec/mafft/mccaskillwrap libexec/mafft/multi2hat3s libexec/mafft/pair2hat3s libexec/mafft/pairash libexec/mafft/pairlocalalign libexec/mafft/regtable2seq libexec/mafft/replaceu libexec/mafft/restoreu libexec/mafft/score libexec/mafft/seekquencer_premafft.pl libexec/mafft/seq2regtable libexec/mafft/setcore libexec/mafft/setdirection libexec/mafft/sextet5 libexec/mafft/splittbfast libexec/mafft/tbfast libexec/mafft/version man/man1/mafft-homologs.1.gz man/man1/mafft.1.gz -%%PORTDOCS%%%%DOCSDIR%%/license %%PORTDOCS%%%%DOCSDIR%%/readme %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.dpparttree %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftns2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.fftnsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.gins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.ginsi.allowshift %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.lins1 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.linsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample.parttree %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.qinsi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/samplerna.xinsi