From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1MlKoe-0007Ao-Ev for garchives@archives.gentoo.org; Wed, 09 Sep 2009 10:54:20 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id CFCFDE08EF; Wed, 9 Sep 2009 10:54:19 +0000 (UTC) Received: from mailout.uni-due.de (mailout.uni-due.de [132.252.185.19]) by pigeon.gentoo.org (Postfix) with ESMTP id 72667E08EF for ; Wed, 9 Sep 2009 10:54:19 +0000 (UTC) Received: from [132.252.170.153] (ce170153.zmb.uni-duisburg-essen.de [132.252.170.153]) (authenticated bits=0) by mailout.uni-due.de (8.13.1/8.13.1) with ESMTP id n89AsIW5009745 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Wed, 9 Sep 2009 12:54:18 +0200 Subject: [gentoo-science] biopython-1.51 From: =?ISO-8859-1?Q?Bj=F6rn?= Thorwirth To: gentoo-science@lists.gentoo.org Content-Type: multipart/mixed; boundary="=-Sy0huRaqJJoze8ArrB0G" Date: Wed, 09 Sep 2009 12:51:45 +0100 Message-Id: <1252497105.25450.1.camel@localhost> Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org Mime-Version: 1.0 X-Mailer: Evolution 2.26.2 X-Spam-Scanned: SpamAssassin: 3.002004 - http://www.spamassassin.org X-Scanned-By: MIMEDefang 2.57 on 132.252.185.19 X-Archives-Salt: c24401e4-8a06-487a-bdb9-e81b27922616 X-Archives-Hash: 51d5a7e8ab4554fd3885a842016d5320 --=-Sy0huRaqJJoze8ArrB0G Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi All! Here is an ebuild for new biopython 1.51. taken and adapted from bug #278130 --=20 Bjoern Thorwirth, Zentrum f=C3=BCr Medizinische Biotechnologie, Universit=C3=A4t Duisburg-Essen, Universit=C3=A4tsstr. 2, 45117 Essen, Ge= rmany phone +49 201 183-4026, bjoern.thorwirth@uni-due.de --=-Sy0huRaqJJoze8ArrB0G Content-Disposition: attachment; filename="biopython-1.51.ebuild" Content-Type: text/plain; name="biopython-1.51.ebuild"; charset="UTF-8" Content-Transfer-Encoding: 7bit # Copyright 1999-2009 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.49.ebuild,v 1.2 2009/07/14 15:31:35 fauli Exp $ NEED_PYTHON=2.4 inherit distutils eutils DESCRIPTION="Biopython - Python modules for computational molecular biology" LICENSE="as-is" HOMEPAGE="http://www.biopython.org" SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" SLOT="0" IUSE="mysql postgres" KEYWORDS="~alpha amd64 ~ppc ~sparc x86" DEPEND="dev-python/numpy >=dev-python/reportlab-2.0 sys-devel/flex" RDEPEND="${DEPEND} mysql? ( dev-python/mysql-python ) postgres? ( dev-python/psycopg )" src_unpack() { unpack ${A} cd "${S}" epatch "${FILESDIR}/${P}-flex.patch" } src_compile() { distutils_src_compile } src_install() { DOCS="CONTRIB DEPRECATED NEWS README" distutils_src_install dodir "/usr/share/doc/${PF}" cp -r Doc/* "${D}/usr/share/doc/${PF}/" || \ die "Failed to install documentation." dodir "/usr/share/${PN}" rm -f Tests/*.pyc || \ die "Failed to remove precompiled test files." cp -r --preserve=mode Scripts Tests "${D}/usr/share/${PN}/" || \ die "Failed to install shared files." } src_test() { cd "${S}/Tests" PYTHONPATH="${PYTHONPATH}:${S}" \ python run_tests.py || die "Tests failed." } --=-Sy0huRaqJJoze8ArrB0G Content-Disposition: attachment; filename="biopython-1.51-flex.patch" Content-Type: text/x-patch; name="biopython-1.51-flex.patch"; charset="UTF-8" Content-Transfer-Encoding: 7bit --- setup.py.old 2008-11-25 18:03:16.000000000 +0100 +++ setup.py 2008-11-25 18:04:14.000000000 +0100 @@ -341,12 +341,12 @@ include_dirs=["Bio"] ), #Commented out due to the build dependency on flex, see Bug 2619 -# Extension('Bio.PDB.mmCIF.MMCIFlex', -# ['Bio/PDB/mmCIF/lex.yy.c', -# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], -# include_dirs=["Bio"], -# libraries=["fl"] -# ), + Extension('Bio.PDB.mmCIF.MMCIFlex', + ['Bio/PDB/mmCIF/lex.yy.c', + 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], + include_dirs=["Bio"], + libraries=["fl"] + ), Extension('Bio.Nexus.cnexus', ['Bio/Nexus/cnexus.c'] ), --=-Sy0huRaqJJoze8ArrB0G--