Received: by mail.netbsd.org (Postfix, from userid 605) id 6AFEF84E18; Fri, 9 Aug 2019 21:52:38 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id E2F0C84E09 for ; Fri, 9 Aug 2019 21:52:37 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id mXeelYz3-3yX for ; Fri, 9 Aug 2019 21:52:34 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 9E57E84E0A for ; Fri, 9 Aug 2019 21:52:34 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 91B53FBF4; Fri, 9 Aug 2019 21:52:34 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1565387554212240" MIME-Version: 1.0 Date: Fri, 9 Aug 2019 21:52:34 +0000 From: "Brook Milligan" Subject: CVS commit: pkgsrc To: pkgsrc-changes@NetBSD.org Reply-To: brook@netbsd.org X-Mailer: log_accum Message-Id: <20190809215234.91B53FBF4@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1565387554212240 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: brook Date: Fri Aug 9 21:52:34 UTC 2019 Modified Files: pkgsrc/biology: Makefile pkgsrc/doc: CHANGES-2019 Added Files: pkgsrc/biology/py-biopython: DESCR Makefile PLIST distinfo Log Message: py-biopython: initial commit The Biopython package contains high-quality, reusable modules and scripts written in Python to make it as easy as possible to use Python for bioinformatics. The Biopython includes the follwing: the ability to parse bioinformatics files into python utilizable data structures, including support for the formats such as Blast output, Clustalw, FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP, Rebase, UniGene, and SwissProt. To generate a diff of this commit: cvs rdiff -u -r1.54 -r1.55 pkgsrc/biology/Makefile cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-biopython/DESCR \ pkgsrc/biology/py-biopython/Makefile pkgsrc/biology/py-biopython/PLIST \ pkgsrc/biology/py-biopython/distinfo cvs rdiff -u -r1.3378 -r1.3379 pkgsrc/doc/CHANGES-2019 Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1565387554212240 Content-Disposition: inline Content-Length: 56609 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/Makefile diff -u pkgsrc/biology/Makefile:1.54 pkgsrc/biology/Makefile:1.55 --- pkgsrc/biology/Makefile:1.54 Fri May 10 16:20:22 2019 +++ pkgsrc/biology/Makefile Fri Aug 9 21:52:34 2019 @@ -1,4 +1,4 @@ -# $NetBSD: Makefile,v 1.54 2019/05/10 16:20:22 bacon Exp $ +# $NetBSD: Makefile,v 1.55 2019/08/09 21:52:34 brook Exp $ # COMMENT= Software for the biological sciences @@ -43,6 +43,7 @@ SUBDIR+= plinkseq SUBDIR+= primer3 SUBDIR+= profit SUBDIR+= puzzle +SUBDIR+= py-biopython SUBDIR+= py-mol SUBDIR+= py-pydicom SUBDIR+= rasmol Index: pkgsrc/doc/CHANGES-2019 diff -u pkgsrc/doc/CHANGES-2019:1.3378 pkgsrc/doc/CHANGES-2019:1.3379 --- pkgsrc/doc/CHANGES-2019:1.3378 Fri Aug 9 20:56:19 2019 +++ pkgsrc/doc/CHANGES-2019 Fri Aug 9 21:52:34 2019 @@ -1,4 +1,4 @@ -$NetBSD: CHANGES-2019,v 1.3378 2019/08/09 20:56:19 brook Exp $ +$NetBSD: CHANGES-2019,v 1.3379 2019/08/09 21:52:34 brook Exp $ Changes to the packages collection and infrastructure in 2019: @@ -5501,3 +5501,4 @@ Changes to the packages collection and i Added www/R-miniUI version 0.1.1.1 [brook 2019-08-09] Added graphics/R-colourpicker version 1.0 [brook 2019-08-09] Added graphics/R-ggExtra version 0.8 [brook 2019-08-09] + Added biology/py-biopython version 1.74 [brook 2019-08-09] Added files: Index: pkgsrc/biology/py-biopython/DESCR diff -u /dev/null pkgsrc/biology/py-biopython/DESCR:1.1 --- /dev/null Fri Aug 9 21:52:34 2019 +++ pkgsrc/biology/py-biopython/DESCR Fri Aug 9 21:52:34 2019 @@ -0,0 +1,7 @@ +The Biopython package contains high-quality, reusable modules and +scripts written in Python to make it as easy as possible to use Python +for bioinformatics. The Biopython includes the follwing: the ability +to parse bioinformatics files into python utilizable data structures, +including support for the formats such as Blast output, Clustalw, +FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP, +Rebase, UniGene, and SwissProt. Index: pkgsrc/biology/py-biopython/Makefile diff -u /dev/null pkgsrc/biology/py-biopython/Makefile:1.1 --- /dev/null Fri Aug 9 21:52:34 2019 +++ pkgsrc/biology/py-biopython/Makefile Fri Aug 9 21:52:34 2019 @@ -0,0 +1,24 @@ +# $NetBSD: Makefile,v 1.1 2019/08/09 21:52:34 brook Exp $ + +DISTNAME= biopython-1.74 +PKGNAME= ${PYPKGPREFIX}-${DISTNAME} +CATEGORIES= biology +MASTER_SITES= http://biopython.org/DIST/ + +MAINTAINER= pkgsrc-users@NetBSD.org +HOMEPAGE= http://biopython.org/ +COMMENT= Python libraries for computational molecular biology +LICENSE= biopython-license + +USE_TOOLS+= pax + +INSTALLATION_DIRS+= share/doc/biopython share/examples/biopython + +post-install: + ${INSTALL_DATA} ${WRKSRC}/README.rst ${DESTDIR}${PREFIX}/share/doc/biopython + ${INSTALL_DATA} ${WRKSRC}/Doc/Tutorial.pdf ${DESTDIR}${PREFIX}/share/doc/biopython + cd ${WRKSRC}/Doc/examples && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/biopython + +.include "../../lang/python/egg.mk" +.include "../../math/py-numpy/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" Index: pkgsrc/biology/py-biopython/PLIST diff -u /dev/null pkgsrc/biology/py-biopython/PLIST:1.1 --- /dev/null Fri Aug 9 21:52:34 2019 +++ pkgsrc/biology/py-biopython/PLIST Fri Aug 9 21:52:34 2019 @@ -0,0 +1,1262 @@ +@comment $NetBSD: PLIST,v 1.1 2019/08/09 21:52:34 brook Exp $ +${PYSITELIB}/${EGG_INFODIR}/PKG-INFO +${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt +${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt +${PYSITELIB}/${EGG_INFODIR}/requires.txt +${PYSITELIB}/${EGG_INFODIR}/top_level.txt +${PYSITELIB}/Bio/Affy/CelFile.py +${PYSITELIB}/Bio/Affy/CelFile.pyc +${PYSITELIB}/Bio/Affy/CelFile.pyo +${PYSITELIB}/Bio/Affy/__init__.py +${PYSITELIB}/Bio/Affy/__init__.pyc +${PYSITELIB}/Bio/Affy/__init__.pyo +${PYSITELIB}/Bio/Align/AlignInfo.py +${PYSITELIB}/Bio/Align/AlignInfo.pyc +${PYSITELIB}/Bio/Align/AlignInfo.pyo +${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.py +${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyc +${PYSITELIB}/Bio/Align/Applications/_ClustalOmega.pyo +${PYSITELIB}/Bio/Align/Applications/_Clustalw.py +${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyc +${PYSITELIB}/Bio/Align/Applications/_Clustalw.pyo +${PYSITELIB}/Bio/Align/Applications/_Dialign.py +${PYSITELIB}/Bio/Align/Applications/_Dialign.pyc +${PYSITELIB}/Bio/Align/Applications/_Dialign.pyo +${PYSITELIB}/Bio/Align/Applications/_MSAProbs.py +${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyc +${PYSITELIB}/Bio/Align/Applications/_MSAProbs.pyo +${PYSITELIB}/Bio/Align/Applications/_Mafft.py +${PYSITELIB}/Bio/Align/Applications/_Mafft.pyc +${PYSITELIB}/Bio/Align/Applications/_Mafft.pyo +${PYSITELIB}/Bio/Align/Applications/_Muscle.py +${PYSITELIB}/Bio/Align/Applications/_Muscle.pyc +${PYSITELIB}/Bio/Align/Applications/_Muscle.pyo +${PYSITELIB}/Bio/Align/Applications/_Prank.py +${PYSITELIB}/Bio/Align/Applications/_Prank.pyc +${PYSITELIB}/Bio/Align/Applications/_Prank.pyo +${PYSITELIB}/Bio/Align/Applications/_Probcons.py 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