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# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar>
# $FreeBSD$
PORTNAME= lagan
PORTVERSION= 2.0
PORTREVISION= 2
CATEGORIES= biology
MASTER_SITES= http://lagan.stanford.edu/lagan_web/
DISTNAME= ${PORTNAME}${PORTVERSION:S/.//}
MAINTAINER= ports@FreeBSD.org
COMMENT= Efficient tools for large-scale multiple alignments of genomic DNA
LICENSE= GPLv2
USES= perl5 shebangfix
USE_PERL5= run
SHEBANG_FILES= slagan.pl
MAKE_JOBS_UNSAFE=yes
CFLAGS+= -fcommon
DEPRECATED= Unmaintained and dead upstream, does not build with -fno-common (llvm 11)
EXPIRATION_DATE=2021-04-01
SUB_FILES= pkg-message
SUB_LIST= LAGAN_DIR="${LAGAN_DIR}"
PLIST_FILES= ${EXECUTABLES:S,^,${PORTNAME}/,} \
${SCRIPTS:S,^,${PORTNAME}/,} \
${EXEUTILS:S,^,${PORTNAME}/utils/,} \
${SCRIPTUTILS:S,^,${PORTNAME}/utils/,} \
${READMES:S,^,${PORTNAME}/Readmes/,}
LAGAN_DIR= ${PREFIX}/${PORTNAME}
EXECUTABLES= anchors chaos glocal mlagan order
SCRIPTS= anal_gloc.pl lagan.pl rechaos.pl slagan.pl
EXEUTILS= Glue bin2bl bin2mf cextract contigorder cstat dotplot fa2xfa \
getbounds getcontigpos getlength getoverlap rc scorealign \
scorecontigs seqmerge
SCRIPTUTILS= cmerge2.pl draft.pl mextract.pl mf2bin.pl mpretty.pl \
mproject.pl mrun.pl mrunfile.pl mrunpairs.pl mviz.pl
READMES= README.FIRST README.chaos README.lagan README.mlagan \
README.tools README.shuffle
post-patch:
@${FIND} ${WRKSRC} -name "Makefile" | ${XARGS} ${REINPLACE_CMD} -e \
'/^CC/s|^|#| ; \
/^CFLAGS/s|^|#| ; \
s|$$(CC) -o|$$(CC) $$(CFLAGS) -o| ; \
s|$$(CPP) -o|$$(CXX) $$(CXXFLAGS) -o| ; \
s|$$(CLINKER) $$(OPTFLAGS)|$$(CXX) $$(LDFLAGS)|'
@${FIND} ${WRKSRC}/src -name "*.c" | ${XARGS} ${REINPLACE_CMD} -e \
's|^inline |static inline |'
do-install:
@${MKDIR} ${STAGEDIR}${LAGAN_DIR}
.for exe in ${EXECUTABLES}
${INSTALL_PROGRAM} ${WRKSRC}/${exe} ${STAGEDIR}${LAGAN_DIR}
.endfor
.for script in ${SCRIPTS}
${INSTALL_SCRIPT} ${WRKSRC}/${script} ${STAGEDIR}${LAGAN_DIR}
.endfor
@${MKDIR} ${STAGEDIR}${LAGAN_DIR}/utils
.for exeutil in ${EXEUTILS}
${INSTALL_PROGRAM} ${WRKSRC}/utils/${exeutil} ${STAGEDIR}${LAGAN_DIR}/utils
.endfor
.for scriptutil in ${SCRIPTUTILS}
${INSTALL_SCRIPT} ${WRKSRC}/utils/${scriptutil} ${STAGEDIR}${LAGAN_DIR}/utils
.endfor
@${MKDIR} ${STAGEDIR}${LAGAN_DIR}/Readmes
.for readme in ${READMES}
${INSTALL_DATA} ${WRKSRC}/Readmes/${readme} ${STAGEDIR}${LAGAN_DIR}/Readmes
.endfor
.include <bsd.port.mk>
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