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PORTNAME= ncbi-toolkit
DISTVERSION= 2017.01.06 # containing BLAST v2.2.27 (? is this true)
PORTREVISION= 6
CATEGORIES= biology
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
DISTNAME= ncbi
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
MAINTAINER= yuri@FreeBSD.org
COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
WWW= https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \
libgmp.so:math/gmp \
libgnutls.so:security/gnutls \
libhogweed.so:security/nettle \
libidn2.so:dns/libidn2 \
libnettle.so:security/nettle \
libp11-kit.so:security/p11-kit \
libpng.so:graphics/png \
libtasn1.so:security/libtasn1 \
libtspi.so:security/trousers \
libunistring.so:devel/libunistring
USES= gettext-runtime iconv jpeg motif xorg
USE_XORG= x11 xau xext xft xmu xrender xt
CONFLICTS_INSTALL= fhist # bin/test_regexp man/man1/fmerge.1.gz
SUB_FILES= pkg-message
OPTIONS_DEFINE= DOCS
post-patch:
@${REINPLACE_CMD} -e \
's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
@${REINPLACE_CMD} -e \
'/^NCBI_CC/s|=.*|= ${CC}| ; \
/^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
/^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
/^NCBI_VIBLIBS/s|-lXp\ || ; \
/^NCBI_DISTVIBLIBS/s|-lXp\ || ; \
s|-I/usr/X11R6/include||g ; \
s|-L/usr/X11R6/lib||g ; \
s|/usr/local|${LOCALBASE}|g ; \
s|-Wl,-Bstatic|| ; \
s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk
@${REINPLACE_CMD} -e 's/%%ICONV_LIB%%/${ICONV_LIB}/' \
${WRKSRC}/make/makeall.unx ${WRKSRC}/make/makenet.unx
# the ncbi-toolkit provides a shell script to drive the build
# and we use it
do-build:
@cd ${WRKDIR} && ./${DISTNAME}/make/makedis.csh
# the ncbi-toolkit does not provide an install target
# we thus roll our own
do-install:
cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin
@${MKDIR} ${STAGEDIR}${PREFIX}/lib/${DISTNAME}
cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a \
${STAGEDIR}${PREFIX}/lib/${DISTNAME}
@${MKDIR} ${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}
cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
${STAGEDIR}${PREFIX}/include/${DISTNAME}/connect
cd ${WRKSRC}/doc/man && ${INSTALL_MAN} * \
${STAGEDIR}${MANPREFIX}/man/man1
@${MKDIR} ${STAGEDIR}${DATADIR}
cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}
do-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
@(cd ${WRKSRC}/doc && \
${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} '-not ( -name man -o -path ./man\/* )')
.include <bsd.port.mk>
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