Upgrade to 1.23.
Approved by: maintainer timeout
This commit is contained in:
Dag-Erling Smørgrav
parent
701be0e9c4
commit
7da5c3b016
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=100524
6 changed files with 1125 additions and 1001 deletions
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@ -6,129 +6,34 @@
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#
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PORTNAME= biopython
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PORTVERSION= 1.00.a4
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PORTVERSION= 1.23
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CATEGORIES= biology python
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MASTER_SITES= http://www.biopython.org/Download/
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MASTER_SITES= http://www.biopython.org/files/
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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DISTNAME= ${PORTNAME}-${PORTVERSION:S/.a/a/}
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DISTFILES= ${DISTNAME}${EXTRACT_SUFX}
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MAINTAINER= wjv@FreeBSD.org
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COMMENT= A collection of Python modules for bioinformatics
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CONFLICTS= py*-martel-*
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BUILD_DEPENDS= ${PYDISTUTILS}
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RUN_DEPENDS= ${PYNUMERIC} \
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${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \
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${PYTHON_SITELIBDIR}/mx/TextTools/__init__.py:${PORTSDIR}/lang/py-mx-base
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USE_PERL5_BUILD=yes
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USE_PYTHON= yes
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USE_PYTHON= 2.0+
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PYTHON_SETUP= ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py
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PLIST_SUB+= PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \
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PLIST_FNORB=${PLIST_FNORB}
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CPIO= cpio --quiet -pdum -R
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EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME}
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# CORBA support (a.k.a Biopython-CORBA):
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# Set WITH_CORBA to enable CORBA support for the Biopython port.
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.if defined(WITH_CORBA)
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# CORBA_ORB may be set from the command line to either "omniorb", "fnorb"
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# or "orbit".
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# - omniORB is a commercial quality, high speed ORB. The installation is
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# huge and building the C++ source is a lengthy process. The omniORBpy
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# Python bindings are used.
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# - Fnorb is a tiny, lightweight ORB and is excellent for testing purposes.
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# Its licence is non-free.
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# - ORBit is a very popular and elegant ORB. The ORBit-Python bindings are
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# used.
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# Note: If unspecified, "orbit" is assumed as default.
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CORBA_ORB?= orbit
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CORBA_VERSION= 0.3.0
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CORBA_DISTNAME= biopython-corba-${CORBA_VERSION}
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CORBA_WRKSRC= ${WRKDIR}/${CORBA_DISTNAME}
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DISTFILES+= ${CORBA_DISTNAME}${EXTRACT_SUFX}
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PLIST_CORBA= ""
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.if ${CORBA_ORB} == "omniorb"
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RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/omniORB/__init__.py:${PORTSDIR}/devel/py-omniorb
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CORBA_ORBNAME= omniORB
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PLIST_OMNIORB= ""
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PLIST_FNORB= "@comment "
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.elif ${CORBA_ORB} == "fnorb"
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BUILD_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
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RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/Fnorb/__init__.py:${PORTSDIR}/devel/fnorb
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CORBA_ORBNAME= Fnorb
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PLIST_OMNIORB= "@comment "
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PLIST_FNORB= ""
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.elif ${CORBA_ORB} == "orbit"
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RUN_DEPENDS+= ${LOCALBASE}/include/orbit-python/orbit-python.h:${PORTSDIR}/devel/py-orbit
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CORBA_ORBNAME= ORBit
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PLIST_OMNIORB= "@comment "
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PLIST_FNORB= "@comment "
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.endif
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.else
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PLIST_CORBA= "@comment "
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PLIST_OMNIORB= "@comment "
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PLIST_FNORB= "@comment "
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.endif # defined(WITH_CORBA)
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.if !defined(WITHOUT_REPORTLAB)
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RUN_DEPENDS+= ${PYTHON_SITELIBDIR}/reportlab/__init__.py:${PORTSDIR}/print/py-reportlab
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.endif
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pre-fetch:
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.if !defined(BATCH) && !defined(WITH_CORBA)
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@ ${CAT} ${FILESDIR}/corba.msg
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.endif
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post-configure:
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.if defined(WITH_CORBA)
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@ ${PERL} -pi.orig -e \
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"/^orb_implementation/ && s/ORBit/${CORBA_ORBNAME}/" \
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${CORBA_WRKSRC}/BioCorba/biocorbaconfig.py
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.endif
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do-build:
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@ cd ${WRKSRC} && ${PYTHON_SETUP} build
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.if defined(WITH_CORBA)
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@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} build
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.endif
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pre-install:
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@ ${SH} ${PKGREQ} INSTALL
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(cd ${WRKSRC} && ${PYTHON_SETUP} build)
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do-install:
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@ cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
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--prefix=${PREFIX}
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.if defined(WITH_CORBA)
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@ cd ${CORBA_WRKSRC} && ${PYTHON_SETUP} install -c -O1 \
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--prefix=${PREFIX}
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.endif
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post-install:
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.if !defined(NOPORTDOCS)
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@ ${MKDIR} ${DOCSDIR}
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.for docfiles in *.pdf *.py *.tex *.txt
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@ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCSDIR}
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.endfor
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@ ${MKDIR} ${EXAMPLESDIR}
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@ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/* ${EXAMPLESDIR}
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@ cd ${WRKSRC}/Scripts && ${FIND} * \
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| ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
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.if defined(WITH_CORBA)
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@ ${MKDIR} ${DOCSDIR}/BioCorba
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.for docfiles in *.html *.pdf *.tex *.txt
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@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCSDIR}/BioCorba
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.endfor
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@ ${MKDIR} ${EXAMPLESDIR}/BioCorba
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@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/examples/* \
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${EXAMPLESDIR}/BioCorba
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@ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* \
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${EXAMPLESDIR}/BioCorba
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.endif # defined(WITH_CORBA)
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.endif # !defined(NOPORTDOCS)
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(cd ${WRKSRC} && ${PYTHON_SETUP} install -c -O1 --prefix=${PREFIX})
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.include <bsd.port.mk>
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@ -1,2 +1 @@
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MD5 (biopython-1.00a4.tar.gz) = bca77b4242c9a8495f60c7475b884c5d
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MD5 (biopython-corba-0.3.0.tar.gz) = 4465f240d22b113314c70b1dc8ebc41c
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MD5 (biopython-1.23.tar.gz) = 45ea628621c6b04d471f029ef5873aaf
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@ -1,12 +0,0 @@
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---------------------------------------------------------------------------
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Biopython is currently being built without CORBA support. If you wish to
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enable the optional CORBA support, set the WITH_CORBA variable, e.g.:
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make WITH_CORBA=yes install
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If you set WITH_CORBA, you may optionally also set the CORBA_ORB variable
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to "omniorb", "fnorb" or "orbit". If you do not, "omniorb" is assumed as
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default.
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Further details are provided in the comments in this port's Makefile.
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---------------------------------------------------------------------------
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@ -1,11 +0,0 @@
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--- setup.py.orig Fri Jul 6 01:55:51 2001
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+++ setup.py Fri Jul 6 18:13:35 2001
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@@ -188,7 +188,7 @@
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# Martel -- for building parsers
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martel_packages = ['Martel']
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# a flag to determine if we should install Martel
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-INSTALL_MARTEL = 1
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+INSTALL_MARTEL = 0
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# -- setup the packages list
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all_packages = biopython_packages
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File diff suppressed because it is too large
Load diff
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@ -1,17 +0,0 @@
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#!/bin/sh
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PATH=$PATH:/usr/local/bin
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if [ "x$1" = "xINSTALL" -o "x$2" = "xINSTALL" ]; then
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PYTHON_GT=`python -c 'import string, sys; \
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print string.split(sys.version)[0] >= "2.0" and 1'`
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if [ "x${PYTHON_GT}" = "x1" ]; then
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exit 0
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else
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echo "-----------------------------------------------------------"
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echo "Biopython requires Python version 2.0 or greater - "
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echo " please update your Python installation before proceeding."
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echo "-----------------------------------------------------------"
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exit 1
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fi
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fi
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