103 lines
3.7 KiB
Makefile
103 lines
3.7 KiB
Makefile
# Created by: tonym
|
|
# $FreeBSD$
|
|
|
|
PORTNAME= ncbi-toolkit
|
|
PORTVERSION= 2012.06.20 # containing BLAST v2.2.27
|
|
CATEGORIES= biology
|
|
MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
|
|
DISTNAME= ncbi
|
|
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
|
|
|
|
MAINTAINER= ports@FreeBSD.org
|
|
COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
|
|
|
|
OPTIONS_DEFINE= DOCS
|
|
|
|
USES= iconv motif
|
|
MAKE_JOBS_UNSAFE= yes
|
|
|
|
SUB_FILES= pkg-message
|
|
|
|
# These are the executables we install.
|
|
#
|
|
# We follow Debian in the separation of the port in three
|
|
# main categories and in the selection of programs that
|
|
# are installed in each case. This Makes Sense (TM).
|
|
# Thus, we drop a handful of programs that are useful only as tests
|
|
# or code examples
|
|
# (credit goes to Aaron Ucko, the Debian maintainer of the NCBI stuff)
|
|
# Right now the port installs all the executables below, this may
|
|
# change in the future with the addition of selectable knobs or
|
|
# new slave ports
|
|
|
|
TOOLKIT_EXE= asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
|
|
checksub debruijn demo_regexp demo_regexp_grep dosimple \
|
|
entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
|
|
gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
|
|
vecscreen
|
|
BLAST_EXE= bl2seq blastall blastcl3 blastclust blastpgp copymat \
|
|
fastacmd formatdb formatrpsdb impala makemat megablast \
|
|
rpsblast seedtop taxblast
|
|
X11_EXE= Nentrez Psequin ddv entrez2 sbtedit udv
|
|
|
|
# and these are the man pages we have
|
|
MAN_FILES= Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
|
|
asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
|
|
copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
|
|
fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
|
|
getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
|
|
taxblast.1 tbl2asn.1 udv.1 vecscreen.1
|
|
|
|
MAN_LINKS= bl2seq blastall blastcl3 blastpgp impala megablast \
|
|
seedtop rpsblast
|
|
|
|
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|= .*|= ${CFLAGS}| ; \
|
|
s|-I/usr/X11R6/include||g ; \
|
|
s|-L/usr/X11R6/lib||g ; \
|
|
s|/usr/local|${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} ${BLAST_EXE} \
|
|
${TOOLKIT_EXE} ${X11_EXE} ${STAGEDIR}${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} ${MAN_FILES} \
|
|
${STAGEDIR}${MANPREFIX}/man/man1)
|
|
.for man in ${MAN_LINKS}
|
|
${LN} -s ${MANPREFIX}/man/man1/blast.1.gz \
|
|
${STAGEDIR}${PREFIX}/man/man1/${man}.1.gz
|
|
.endfor
|
|
@${MKDIR} ${STAGEDIR}${DATADIR}
|
|
(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR})
|
|
@${MKDIR} ${STAGEDIR}${DOCSDIR}
|
|
@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
|
|
(cd ${STAGEDIR}${DOCSDIR} && ${TAR} --unlink -xf -)
|
|
@${FIND} ${STAGEDIR}${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
|
|
@${FIND} ${STAGEDIR}${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
|
|
|
|
.include <bsd.port.mk>
|