diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index faddb1e0ed5e..0f9389e1d37f 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -6,23 +6,121 @@ # PORTNAME= biopython -PORTVERSION= 0.90.d03 +PORTVERSION= 1.00.a1 CATEGORIES= biology python MASTER_SITES= http://www.biopython.org/Download/ -PKGNAMEPREFIX= py- -DISTNAME= biopython-0.90-d03 +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} +DISTNAME= ${PORTNAME}-${PORTVERSION:S/.a/a/} +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} -MAINTAINER= johann@egenetics.com +MAINTAINER= wjv@FreeBSD.org -USE_PYTHON= yes - -BUILD_DEPENDS= ${PYDISTUTILS} \ +BUILD_DEPENDS= ${PYDISTUTILS} +RUN_DEPENDS= ${PYTHON_SITELIBDIR}/Martel/__init__.py:${PORTSDIR}/textproc/py-martel \ ${PYTHON_SITELIBDIR}/Numeric/Numeric.py:${PORTSDIR}/math/py-numeric +# Biopython requires Python 2.0 or above: +PYTHON_VERSION= python2.1 + +PLIST_SUB+= PLIST_CORBA=${PLIST_CORBA} PLIST_OMNIORB=${PLIST_OMNIORB} \ + PLIST_FNORB=${PLIST_FNORB} +CPIO= cpio --quiet -pdum -R +DOCDIR= ${PREFIX}/share/doc/py-biopython +EGDIR= ${PREFIX}/share/examples/py-biopython + +# CORBA support (a.k.a Biopython-CORBA): +# Set WITH_CORBA to enable CORBA support for the Biopython port. +.if defined(WITH_CORBA) + +# CORBA_ORB may be set from the command line to either "omniorb", "fnorb" +# or "orbit". +# - omniORB is a commercial quality, high speed ORB. The installation is +# huge and building the C++ source is a lengthy process. The omniORBpy +# Python bindings are used. +# - Fnorb is a tiny, lightweight ORB and is excellent for testing purposes. +# - ORBit is a very popular and elegant ORB. The ORBit-Python bindings are +# used. +# Since Fnorb is distributed under a non-free licence and ORBit support in +# Biopython-CORBA is not yet stable, "omniorb" is the default. +CORBA_ORB?= omniorb + +CORBA_VERSION= 0.2.1 +CORBA_DISTNAME= biopython-corba-${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 +CORBA_ORBNAME= Fnorb +EXTRA_PATCHES+= ${PATCHDIR}/extra-patch-build_helper.py +PLIST_OMNIORB= "@comment " +PLIST_FNORB= "" +.elif ${CORBA_ORB} == "orbit" +RUN_DEPENDS+= ${PREFIX}/include/orbit-python/orbit-python.h:${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) + +pre-fetch: +.if !defined(BATCH) && !defined(WITH_CORBA) + @ ${CAT} files/corba.msg +.endif + +post-configure: +.if defined(WITH_CORBA) + @ ${PERL} -pi.orig -e \ + "/^orb_implementation/ && s/omniORB/${CORBA_ORBNAME}/" \ + ${CORBA_WRKSRC}/BioCorba/biocorbaconfig.py +.endif + do-build: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py build) + @ cd ${WRKSRC} && ${PYTHON_CMD} setup.py build +.if defined(WITH_CORBA) + @ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py build +.endif do-install: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup.py install) + @ cd ${WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \ + --prefix=${PREFIX} +.if defined(WITH_CORBA) + @ cd ${CORBA_WRKSRC} && ${PYTHON_CMD} setup.py install -c -O1 \ + --prefix=${PREFIX} +.endif + +post-install: +.if !defined(NOPORTDOCS) + @ ${MKDIR} ${DOCDIR} +.for docfiles in *.txt *.tex *.py + @ ${INSTALL_DATA} ${WRKSRC}/Doc/${docfiles} ${DOCDIR} +.endfor + @ ${MKDIR} ${EGDIR} + @ ${INSTALL_DATA} ${WRKSRC}/Doc/examples/*.py ${EGDIR} + @ cd ${WRKSRC} && find Scripts \ + | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR} +.if defined(WITH_CORBA) + @ ${MKDIR} ${DOCDIR}/BioCorba +.for docfiles in *.tex *.pdf + @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Doc/${docfiles} ${DOCDIR}/BioCorba +.endfor + @ ${MKDIR} ${EGDIR}/BioCorba + @ cd ${CORBA_WRKSRC}/Doc/examples && find * \ + | ${CPIO} ${SHAREOWN}:${SHAREGRP} ${EGDIR}/BioCorba + @ ${MKDIR} ${EGDIR}/BioCorba/Scripts + @ ${INSTALL_DATA} ${CORBA_WRKSRC}/Scripts/* ${EGDIR}/BioCorba/Scripts +.endif # defined(WITH_CORBA) +.endif # !defined(NOPORTDOCS) .include diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo index 3f2f59443b92..a0b94229746a 100644 --- a/biology/py-biopython/distinfo +++ b/biology/py-biopython/distinfo @@ -1 +1,2 @@ -MD5 (biopython-0.90-d03.tar.gz) = 6eba4ef18fee09f47c127d44667a3d5c +MD5 (biopython-1.00a1.tar.gz) = 054baa272e2885e17512964215817119 +MD5 (biopython-corba-0.2.1.tar.gz) = 3d6d3e4570ff2996bef84e08f6fabc25 diff --git a/biology/py-biopython/files/corba.msg b/biology/py-biopython/files/corba.msg new file mode 100644 index 000000000000..df7961e5b5a4 --- /dev/null +++ b/biology/py-biopython/files/corba.msg @@ -0,0 +1,12 @@ +--------------------------------------------------------------------------- +Biopython is currently being built without CORBA support. If you wish to +enable the optional CORBA support, set the WITH_CORBA variable, e.g.: + + make WITH_CORBA=yes install + +If you set WITH_CORBA, you may optionally also set the CORBA_ORB variable +to "omniorb", "fnorb" or "orbit". If you do not, "omniorb" is assumed as +default. + +Further details are provided in the comments in this port's Makefile. +--------------------------------------------------------------------------- diff --git a/biology/py-biopython/files/extra-patch-build_helper.py b/biology/py-biopython/files/extra-patch-build_helper.py new file mode 100644 index 000000000000..777e20947f5d --- /dev/null +++ b/biology/py-biopython/files/extra-patch-build_helper.py @@ -0,0 +1,24 @@ +Nasty, nasty workaround for an error which I can't quite explain. This +happens only if Fnorb is chosen as CORBA ORB. Since CORBA support itself +is optional in this port, this patch is added to EXTRA_PATCHES only if +necessary. + +-- Johann Visagie + + +--- ../biopython-corba-0.2.1/build_helper.py.orig Sun Apr 15 15:19:31 2001 ++++ ../biopython-corba-0.2.1/build_helper.py Thu Jun 7 16:25:05 2001 +@@ -125,7 +125,12 @@ + # move the new file in place of the old + input_handle.close() + output_handle.close() +- os.rename(output_file, file) ++ input_handle = open(output_file, 'r') ++ output_handle = open(file, 'w') ++ S = input_handle.read() ++ output_handle.write(S) ++ input_handle.close() ++ output_handle.close() + + def generate_orbit_stubs(idl_name, remove_old = 1): + """Move adapters to act as stubs and skeletons for ORBit. diff --git a/biology/py-biopython/pkg-descr b/biology/py-biopython/pkg-descr index 2216005d2351..c122f25cc2d3 100644 --- a/biology/py-biopython/pkg-descr +++ b/biology/py-biopython/pkg-descr @@ -1,12 +1,15 @@ -The Biopython Project is an international association of developers of freely -available Python tools for use in areas of computational molecular biology -such as bioinformatics and genomics. +The Biopython Project is an international association of developers who are +providing freely available Python tools for use in areas of computational +molecular biology such as bioinformatics and genomics. Biopython is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics -applications in the Python language. It is currently in developer's -(pre-alpha) release. Caveat emptor. +applications in the Python language. -WWW: http://www.biopython.org/ +Note that the current release is alpha quality, and not yet deemed to be +stable. + +Authors: +WWW: http://biopython.org/ -- Johann Visagie diff --git a/biology/py-biopython/pkg-plist b/biology/py-biopython/pkg-plist index 3aa022327daa..0682a5f9fa13 100644 --- a/biology/py-biopython/pkg-plist +++ b/biology/py-biopython/pkg-plist @@ -1,143 +1,572 @@ -lib/%%PYTHON_VERSION%%/site-packages/Bio/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/ParserSupport.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Seq.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Index.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/PropertyManager.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/File.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Sequence.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/utils.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SeqRecord.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/KeyWList.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/SwissProt/SProt.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/NCBIWWW.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/Record.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Blast/NCBIStandalone.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Enzyme/Enzyme.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Fasta/Fasta.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/PDB/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite/__init__.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite/Prosite.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite/Pattern.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Prosite/Prodoc.py -lib/%%PYTHON_VERSION%%/site-packages/Bio/Medline/Medline.py 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