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# New ports collection makefile for: py-biopython
# Date created: 28 July 2000
# Whom: Johann Visagie <johann@egenetics.com>
#
# $FreeBSD$
#
PORTNAME= biopython
PORTVERSION= 1.00.a4
CATEGORIES= biology python
MASTER_SITES= http://www.biopython.org/Download/
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
DISTNAME= ${PORTNAME}-${PORTVERSION:S/.a/a/}
DISTFILES= ${DISTNAME}${EXTRACT_SUFX}
MAINTAINER= wjv@FreeBSD.org
COMMENT= A collection of Python modules for bioinformatics
BUILD_DEPENDS= ${PYDISTUTILS}
RUN_DEPENDS= ${PYNUMERIC} \
${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \
${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
USE_PYTHON= yes
PYTHON_SETUP= ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
PLIST_SUB+= PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \
PLIST_FNORB=${PLIST_FNORB}
CPIO= cpio --quiet -pdum -R
EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME}
# CORBA support (a.k.a Biopython-CORBA):
# Set WITH_CORBA to enable CORBA support for the Biopython port.
.if defined(WITH_CORBA)
# CORBA_ORB may be set from the command line to either "omniorb", "fnorb"
# or "orbit".
# - omniORB is a commercial quality, high speed ORB. The installation is
# huge and building the C++ source is a lengthy process. The omniORBpy
# Python bindings are used.
# - Fnorb is a tiny, lightweight ORB and is excellent for testing purposes.
# Its licence is non-free.
# - ORBit is a very popular and elegant ORB. The ORBit-Python bindings are
# used.
# Note: If unspecified, "orbit" is assumed as default.
CORBA_ORB?= orbit
CORBA_VERSION= 0.3.0
CORBA_DISTNAME= biopython-corba-${CORBA_VERSION}
CORBA_WRKSRC= ${WRKDIR}/${CORBA_DISTNAME}
DISTFILES+= ${CORBA_DISTNAME}${EXTRACT_SUFX}
PLIST_CORBA= ""
.if ${CORBA_ORB} == "omniorb"
RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/omniORB/__init__.py:${PORTSDIR}/devel/py-omniorb
CORBA_ORBNAME= omniORB
PLIST_OMNIORB= ""
PLIST_FNORB= "@comment "
.elif ${CORBA_ORB} == "fnorb"
BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
CORBA_ORBNAME= Fnorb
PLIST_OMNIORB= "@comment "
PLIST_FNORB= ""
.elif ${CORBA_ORB} == "orbit"
RUN_DEPENDS+= ${LOCALBASE}/include/orbit-python/orbit-python.h:${PORTSDIR}/devel/py-orbit
CORBA_ORBNAME= ORBit
PLIST_OMNIORB= "@comment "
PLIST_FNORB= "@comment "
.endif
.else
PLIST_CORBA= "@comment "
PLIST_OMNIORB= "@comment "
PLIST_FNORB= "@comment "
.endif # defined(WITH_CORBA)
.if !defined(WITHOUT_REPORTLAB)
RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
.endif
pre-fetch:
.if !defined(BATCH) && !defined(WITH_CORBA)
@ ${CAT} ${FILESDIR}/corba.msg
.endif
post-configure:
.if defined(WITH_CORBA)
@ ${PERL} -pi.orig -e \
"/^orb_implementation/ && s/ORBit/${CORBA_ORBNAME}/" \
${CORBA_WRKSRC}/BioCorba/biocorbaconfig.py
.endif
do-build:
@ cd ${WRKSRC} && ${PYTHON_SETUP} build
.if defined(WITH_CORBA)
@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} build
.endif
pre-install:
@ ${SH} ${PKGREQ} INSTALL
do-install:
@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
--prefix=${PREFIX}
.if defined(WITH_CORBA)
@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
--prefix=${PREFIX}
.endif
post-install:
.if !defined(NOPORTDOCS)
@ ${MKDIR} ${DOCSDIR}
.for docfiles in *.pdf *.py *.tex *.txt
@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
.endfor
@ ${MKDIR} ${EXAMPLESDIR}
@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/* ${EXAMPLESDIR}
@ cd ${WRKSRC}/Scripts && find * \
| ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
.if defined(WITH_CORBA)
@ ${MKDIR} ${DOCSDIR}/BioCorba
.for docfiles in *.html *.pdf *.tex *.txt
@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
.endfor
@ ${MKDIR} ${EXAMPLESDIR}/BioCorba
@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/examples/* \
${EXAMPLESDIR}/BioCorba
@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
${EXAMPLESDIR}/BioCorba
.endif # defined(WITH_CORBA)
.endif # !defined(NOPORTDOCS)
.include <bsd.port.mk>
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